WebChemistry Wiki - User contributions [en]

LiteMol:SelectionAlgebra

2017-05-05T12:23:12Z

Matthew: edited by MJC

LiteMol has an atom selection language available, similar to other structure visualization tools such as VMD or PyMOL. The '''LiteMol selection algebra''' is inspired by our other service - [[PatternQuery:UserManual | PatternQuery]]. While in the present version the selection syntax will be mainly used by method developers, syntax enabling the use of [[LiteMol:SelectionAlgebra#PyMOL | PyMOL ]] and possibly [[LiteMol:SelectionAlgebra#VMD| VMD]] selection algebra will be introduced in the near future.

=LiteMol selection algebra=

Molecular selections can be created in two different active contexts - [[LiteMol:Hierarchy#Molecule_Model_.28MM.29 | model of molecule]] or [[LiteMol:Hierarchy#Molecule_Visual_.28VM.29 | molecule visual]]. If either of the contexts is active in the entity tree, the right panel is populated with the '''Selection''' action. Next, you can create a named selection using the dedicated query language and further modify the visual part of your selection.

{{large| '''Notice:'''}} Arguments of LiteMol selection queries are '''case sensitive'''!

Meaning: '''GLY''' is a common non-polar residue found in PDB entries, whereas '''Gly''', '''gly''', or '''G''' do not exist.

==Basic queries==
{| class="wikitable"
! colspan="3" | List of selection queries
|-
!Query definition
!Example
!Selection description
|-
| <code> atomsByElement(elements: string[]) </code >
| <code> atomsByElement('C'), atomsByElement('C','O') </code>
| Atoms based on their element symbol (field ''_atom_site.type_symbol'').
|-
| <code> atomsByName(elements: string[]) </code>
| <code> atomsByName('C'), atomsByName('N','CA','C','O') </code>
| Atoms based on their atom name (field ''_atom_site.label_atom_id'').
|-
| <code> atomsById(numbers: number[]) </code>
| <code> atomsById(1), atomsById(1,2,3) </code>
| Atoms based on their integer identifier (field ''_atom_site.id '').
|-
| <code> residuesByName(elements: string[]) </code>
| <code> residuesByName('GLY'), residuesByName('ALA', 'PO4') </code>
| Residues based on their residue name (field ''_atom_site.label_comp_id'').
|-
| <code> residuesById(numbers: number[]) </code>
| <code> residuesById(100), residuesById(42,157,238) </code>
| Residues based on integer identified (field ''_atom_site.auth_seq_id'').
|-
| <code> chainsById(elements: string[]) </code>
| <code> chainsById('A'), chainsById('A', 'B') </code>
| Polymer chains based on their id (field ''_atom_site.auth_asym_id'').
|-
| <code> backbone() </code>
| <code> backbone() </code>
| Extracts structure backbone defined by certain atom names. '''Protein:''' ''N'', ''CA'', ''C'', ''O''. '''Nucleotide:''' ''P'', ''OP1'', ''OP2'', ''O3' '', ''O5' '', ''C3' '', ''C5' ''.
|-
| <code> sidechain() </code>
| <code> sidechain() </code>
| Complement to the previous query, i.e. all ''polymer'' atoms without such name are reported.
|-
| <code> hetGroups() </code>
| <code> hetGroups() </code>
| ''HETATM'' atoms defined by the field ''_atom_site.group_PDB''.
|-
| <code> nonHetPolymer() </code>
| <code> nonHetPolymer() </code>
| ''ATOM'' atoms defined by the field ''_atom_site.group_PDB''.
|-
|<code> cartoon() </code>
|<code> cartoon() </code>
| Extracts atoms vital for ''polymer'' cartoon visualization based on their names: ''CA'', ''O'', ''O5' '', ''C3' '', ''N3''.
|-
| <code> everything() </code>
| <code> everything() </code>
| All atoms in the active context.
|-
|}

==Advanced queries==
{| class="wikitable"
! colspan="3" | List of selection queries
|-
!
Query
!
Examples
!
Selection description
|-
| <code> inside(where: Selection, sel: Selection) </code>
| <code> residuesByName('GLY').inside(chainsById('A')) </code>
| Finds selection within another selection.
|-
| <code> ambientResidues(where: Selection, nmb: number ) </code>
| <code> residuesByName('HEM').ambientResidues(5) </code>
| Surrounds the inner selection by residues that have at least one atom within the given radius
|-
| <code> wholeResidues(where: Selection) </code>
| <code> atomsByElement('Pt').wholeResidues() </code>
| Surrounds the inner selection by all atoms of residue's origin.
|-
|}

==Logical queries==
{| class="wikitable"
! colspan="3" | List of selection queries
|-
!Query
!Examples
!Selection description
|-
| <code> or(selections: Selection[]) </code>
| <code> or(residuesByName('HEM').ambientResidues(5), chainsById('A')) </code>
| Merges several selections.
|-
| <code> intersectWith(where: Selection, sel: Selection) </code>
| <code> residuesByName('HEM').ambientResidues(5).intersectWith(chainsById('A')) </code>
| Finds intersection between two selections.
|-
| <code> complement(where: Selection) </code>
| <code> chainsById('A').complement() </code>
| Finds the complement of the inner selection to the active context.
|-
|}

LiteMol:Functionality

2017-05-05T12:18:21Z

Matthew: /* Classic features */ mjc

{{large| '''LiteMol is a powerful and blazing-fast cross-platform tool for handling 3D macromolecular data in the browser. [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ Try it now!]'''}}

=Classic features=
* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).
* All common visualization models ('balls-and-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).
* Displays electron densities for X-ray crystallographic structures and electronic potential maps for cryo-EM models.
* Available as a [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ standalone viewer] or as a [https://github.com/dsehnal/LiteMol library} for embedding into third party applications.

[[Image:LiteMol-Models.png|center|800px]]

=Advanced features=
* Introduces the [https://github.com/dsehnal/BinaryCIF BinaryCIF] a compression format compatible with standard PDBx/mmCIF format ''greatly reducing'' the amount of transferred data.
* [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] allows for streaming only those parts of the structural model relevant for the user required visualization. This further ''decreases'' the amount of ''transferred data'' and facilitates ''near instant responsiveness'' even for huge structures such as ribosomes and viral capsids. All in your web browser.
* [http://webchem.ncbr.muni.cz/DensityServer DensityServer ] allows ''instant access'' to full resolution user determined slices of ''electron density'' (e.g. binding sites) and down sampled surface of the entire biomacromolecular structure.
* Displays [https://www.wwpdb.org/validation/validation-reports wwPDB validation reports] and [[ValidatorDB:UserManual | ValidatorDB ligand validation]].
* Displays ''sequence annotations'' from [http://pfam.xfam.org/ Pfam], [https://www.ebi.ac.uk/interpro/ InterPro], [www.cathdb.info CATH], [http://scop.berkeley.edu/ SCOP], [http://www.uniprot.org/ UniProt].
* Visualizer requires only an up-to-date ''web browser'' with no dependencies required. Runs on all ''mobile devices''.
* Minimal ''memory footprint''.

[[Image:LiteMol-Performance.png|center|800px]]

LiteMol:Hierarchy

2017-05-05T12:08:42Z

Matthew: /* Raw Data */ mjc

[[File:LiteMol-hierarchy.png | thumb | 200px | right| An example of an '''entity tree'''. ]]

All data in LiteMol are organized in a hierarchy represented by the '''entity tree'''. This tree is shown in LiteMol's left panel. When you click on an entity in the tree, you will see all actions applicable to this entity listed in the right panel.

This page lists all types of entities and explains the actions they provide. The entity types can be divided into four sections: Structures, Visualization, Annotations, and Raw Data.

=Structures=

This section describes the entities used for representation of molecular models and electron density maps. It does not contain any information about how these data are visualized.

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set:
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file.
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action.
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.

==Molecule (M)==

A '''Molecule''' entity represents a set of structural data for a '''Molecule''' (which corresponds to one PDB entry or one mmCIF file).

Applicable actions:
* '''Model''' – Creates a model of the molecule ([[LiteMol:Hierarchy#Molecule Model (MM) |Molecule Model]] entity). Some PDB entries (mostly NMR structures) contain multiple models, in such case, the sequential number ('''Index''') of the desired model to be displayed can be specified.
* '''Density Streaming''' - Creates a [[LiteMol:Hierarchy#Density Streaming (BDS) |Density Streaming]] for this molecule. Clicking on an atom or residue in the structure will instantly download and display the density data for the surrounding region. This solution is, in general, much faster than downloading the whole density map (often more than 1 GB). More details are available [http://webchem.ncbr.muni.cz/DensityServer here].
* '''PDBe Validation Report''' – Downloads wwPDB validation data for this molecule from PDBe and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''Ligand Validation Report''' - Downloads validation data for the ligands in this molecule from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB] and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''PDBe Sequence Annotations''' – Downloads sequence annotation data for this molecule from PDBe (collected from sources such as UniProt, InterProt, Pfam etc.) and creates a [[LiteMol:Hierarchy#Sequence Annotations (SA) | Sequence Annotations]] entity.

==Molecule Model (MM)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create an assembly (e.g. a virus capsid). Alternatively, just a part of the model can constitute a relevant assembly (e.g. the model contains a two molecules while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in the crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstrom) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for structures determined by NMR.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. This option is less automatic than '''Macromolecule Visual''' but more flexible. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding volume will be downloaded instantly. This can be useful when a part of the structure has already been downloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains to display the binding site).
* '''Update Model''' – Applicable when multiple models are included in the PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with the specified index (model number). Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model in addition to the current model.

 

==Group (G)==

This type of entity is used to organize multiple entities that are logically connected. For example, a group of selections containing different parts of a model (protein, ligand, and water) or a group of sequence annotations obtained from the same database.

==Molecule Model Selection (SM)==

This is an entity representing a subset of a molecule model. An example is one protein chain, one atom, or a set of all alanine residues. A selection can be created from either a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] entity or a [[LiteMol:Hierarchy#Molecule Visual (VM) | Molecule Visual]] entity. Selections are created using [[LiteMol:SelectionAlgebra | selection algebra language]].

Applicable actions:
* '''Visual''' – Create a visual representation of this selection. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Update Selection''' - Change the name of the [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] or change its definition using [[LiteMol:SelectionAlgebra | selection algebra language]]. (This action may not be not available for automatically generated selections.)

==Density Data (DD)==

Represents a three-dimensional map of electron density (for X-ray crystal structures) or electronic potential maps (for cryo-EM structures). Two types of maps are available for most crystal structures where structure factors are available in the PDB archive: '''2Fo-Fc''' and '''Fo-Fc'''.

Applicable actions:
* '''Surface''' – Creates a visualization of the density isosurface with the defined isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) |Density Visual]] entity).
* '''Interactive Surface''' – Creates a density isosurface which is shown only for a region of the molecule when you click on that region ([[LiteMol:Hierarchy#Interactive Surface (BIS) |Interactive Surface]] entity).
* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.

=Visualization=

This section contains entities that represent different visualizations of molecules and electron density maps.

==Molecule Visual (VM)==

[[File:LiteMol-cartoon.png | thumb | 250px | right| '''Cartoon''' visual for 1CBS. ]]

[[File:LiteMol-CA_trace.png | thumb | 250px | right| '''C-α trace''' visual for 1CBS. ]]

[[File:LiteMol-balls_and_sticks.png | thumb | 250px | right| '''Balls and Sticks''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-VDW_balls.png | thumb | 250px | right| '''VDW Balls''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-surface.png | thumb | 250px | right| '''Surface''' visual for 1CBS. ]]

A '''Molecule Visual''' is simply a visualization of a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] or its part. It is defined mostly by its type and coloring. These can be changed in '''Update Visual''' action. Click on the “+” icon next to “Type” or “Coloring” to modify other attributes. Some attributes are only available for certain types of visualization.

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Update Visual''' – Allows you to change the type of visualization and other attributes.

List of attributes:
* '''Type''' – One of the following:
** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, strands, and unstructured regions.
** '''C-α Trace''' – Simplified wire-like representation of the backbone (no side-chains).
** '''Balls and Sticks''' – Atoms are represented by balls, bonds are shown as sticks connecting them. Keep in mind that most structures from X-ray and cryo-EM experiments do not provide positions of hydrogen atoms, so these are not visible in '''Ball and Sticks''' representation. There are some extra attributes that you can modify:
*** '''VDW''' – Indicates whether all atoms are shown as spheres with uniform radius ('''VDW''' = Off) or the radius of the sphere radius is based on the element's Van der Waals radius ('''VDW''' = On).
*** '''Scale''' – (Only when '''VDW''' = On) The ratio between the sphere radius and the element's Van der Waals radius.
*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the sphere in Angstrom.
*** '''Bond Rds''' – The width (radius) of the sticks.
*** '''Bond''' – Color of the sticks.
** '''VDW Balls''' – Shows atoms as spheres width radii corresponding to their Van der Waals radii.
** '''Surface''' – Shows the smoothed boundary surface of the space “filled” by the molecule. There are some extra attributes that you can modify:
*** '''Probe Radius''' – How much space around an atom is considered as “filled” by this atom.
*** '''Smoothing''' – With lower values, curvature of the surface around individual atoms will be more noticeable. With higher values the surface will be smoother.
*** '''Auto Detail''' - If set to On, the optimal level of detail is automatically derived from the size of the molecule. If set to Off, the level of detail can be adjusted manually (see the next item).
*** '''Detail''' – Defines precisely how the surface should be visualized. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource demanding) when visualizing larger molecules.
*** '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).
* '''Detail''' – Defines how precisely the molecule should be visualized and can range from '''Very Low''' to '''Very High'''. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource demanding) when visualizing larger molecules. If you choose '''Automatic''', LiteMol will infer the optimal level of detail from the molecule's size.
* '''Coloring''' – One of the following:
** '''Chain ID''' – Every chain will be shown in a different color.
** '''Entity ID''' – The same as '''Chain ID''' but chemically identical chains are shown in the same color.
** '''Entity Type''' – Every type of entity (polymer, non-polymer, water) is shown in a different color.
** '''Residue Name''' – A different color is used for each type of residue.
** '''Element Symbol''' – A different color is used for each element.
** '''Rainbow (Chain)''' - Colors each chain in the colors of rainbow from N-terminus (red) to C-terminus (violet) (or from 5' to 3' in nucleic acids).
** '''Rainbow (Entity)''' - Similar to '''Rainbow (Chain)''', but chemically identical chains are treated as a single longer chain (e.g. in a homodimer).
** '''Uniform Color''' – One selected color is used for the whole '''Visual'''.
* '''Highlight''' – The color in which this '''Visual''' will be temporarily colored when hovering over the '''Visual''' entity in the entity tree. When the cursor is placed on an atom or residue, it will be colored in the same way.
* '''Selection''' – If you create a [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] from this '''Visual''', it will be distinguished from the rest of the '''Visual''' by having this color.
* '''Opacity''' – The level of transparency of the '''Visual'''. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).

Please keep in mind that changing the type of a '''Visual''' will in fact remove the current visual and replace it with a new one, so all changes you have applied to the current '''Visual''' (such as creating a selection from it) will be lost! You can go to the superior entity and create a new '''Visual''' besides the current '''Visual'''.

 

==Density Visual (VDD)==

[[File:LiteMol-density_visual.png | thumb | 250px | right| Density isosurface at 1.5 σ (2Fo-Fc). ]]

Represents an isosurface of electron density, i.e. the surface in 3D connecting all the points with the value of electron density equal to a specified isovalue.

Applicable actions:
* '''Update Surface''' – Allows you to change the attributes of the visualization.

List of attributes:
* '''Iso value''' – The isovalue of electron density used for the visualized surface.
* '''Relative''' - Indicates whether normalized ('''Relative''' = On) or unnormalized ('''Relative''' = Off) density values are used. The relationship between the two values is as follows: ''Normalized'' = (''Unnormalized'' - ''Mean'') / ''Sigma''.
* '''Color''' – The color of the surface.
* '''Opacity''' – The level of transparency of the surface. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).
* '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).

 
==Interactive Surface (BIS)==

[[File:LiteMol-interactive_surface.png | thumb | 250px | right| Interactive density isosurface at 1.5 σ (2Fo-Fc) shown for a tryptophan residue and its surroundings with radius 2 Angstroms. ]]

This is a visualization of an isosurface of electron density, just as [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]]. The difference is that this surface is shown only when you click on a residue or an atom in the structure. The surface is shown only for the region around the selected residue or atom. An advantage of this interactive visualization is that the relevant region of density surface is not hindered by the rest of the molecule.

Three default '''Interactive Surfaces''' are created automatically when loading density data: blue surface corresponds to isovalue 1.5 in 2Fo-Fc density map. Green and red surfaces correspond to isovalues +3 and -3 in Fo-Fc difference density maps.

Applicable actions:
* '''Update Interactive Surface''' – Change the attributes of the visualization. These attributes are the same as in the case of [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity. An extra attribute is '''Radius''', which allows you to change the size of the region for which the isosurface is shown. Attribute '''Show''' toggles between interactive visualization around the selected region ('''Show''' = Around Selection) and static visualization of the whole map ('''Show''' = Everything, practically equivalent to [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity).

 

=Annotations=

This section describes entities which can store additional information about the structures, such as validation issues or sequence annotations.

==Validation Report (VR)==

[[File:LiteMol-validation_report.png | thumb | 250px | right| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]

[[File:LiteMol-ligand_validation_report.png | thumb | 250px | right| An oligosaccharide in the structure of ribosome-inactivating protein abrin-a (1ABR) colored by the '''Ligand Validation Report'''. The right-most residue is missing an atom. One of the residues in the center has an atom with which is the chirality. ]]

Represents geometric validation data for this molecule from the wwPDB validation report. The full validation report in PDF can be downloaded from the [http://www.ebi.ac.uk/pdbe/ PDBe site] (find your molecule, click ''Details'' in ''Experiments and Validation'' section, and then ''Full Validation Report'' in the right panel). An example of a validation report is available [http://www.ebi.ac.uk/pdbe/entry-files/download/1rtc_full_validation.pdf here].

Another type of '''Validation Report''' entity is '''Ligand Validation Report''', which represents validation data for the ligands in this structure. These data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB].

Applicable actions:
* '''Apply Coloring''' – The structure will be colored according the validation data. For '''PDBe Validation Report''' the color of each residue depends on the number of geometric outliers it contains: green = 0, yellow = 1, orange = 2, and red = 3 or more. For '''Ligand Validation Report''' the residues with missing atoms are colored in red. Also the atoms with wrong chirality are shown in red (examples can be found in PDB entry 1ABR). Correct residues are shown in green.

 

==Sequence Annotations (SA)==

[[File:LiteMol-annotation.png | thumb | 250px | right| Structure of ricin A chain (4Q2V). The orange color indicates the part annotated as ''Ribosome-inactivating protein, subdomain 1'' by InterPro database. ]]

Represents a collection of sequence annotations via the PDBe API, grouped by the source database.

==Sequence Annotation (SA)==

Represents a single sequence annotation, i.e. assignment of a name to a part of the structure. When you hover above this entity or click on it, the corresponding part of the structure will be shown in a distinctive color.

Applicable actions:
* '''Update PDBe Sequence Annotation''' – Allows you to change the color used for this part of the structure.

 
=Raw Data=

This section contains entities that store data from a file, no matter what these data represent and how they are encoded (i.e. original data from a file before they are parsed). The user will encounter them mostly when loading files from a disk or a URL.

==String Data (SD)==
This entity represents data loaded from a file in textual format (e.g. mmCIF file or PDB file).

Applicable actions:
* '''Molecule''' – Treats the data as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. Make sure to select the appropriate format.
* '''Density Data''' – Treats the data as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity.
* '''CIF Dictionary''' – Treats the data as a CIF dictionary and creates a [[LiteMol:Hierarchy#CIF Dictionary (CD) | CIF Dictionary]] entity. CIF dictionary itself can contain various kinds of data, including molecular structures or density maps.

==Binary Data (BD)==
This entity represents data loaded from a binary file (not human-readable, e.g. [https://github.com/dsehnal/BinaryCIF BinaryCIF] file or CCP4 density file). '''Binary Data''' provides exactly the same actions as [[LiteMol:Hierarchy#String Data (SD) | String Data]].

==CIF Dictionary (CD)==
This entity represents data encoded in a CIF dictionary, which is a flexible format for various kinds of data, so it can contain molecular structures or density maps. A single CIF dictionary can even contain multiple objects (e.g. two density maps: 2Fo-Fc and Fo-Fc).

Applicable actions:
* '''Molecule''' – Treats the data in the '''CIF dictionary''' as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').
* '''Density Data''' – Treats the data in the '''CIF dictionary''' as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').

LiteMol:Hierarchy

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Matthew: /* Sequence Annotations (SA) */ mjc

[[File:LiteMol-hierarchy.png | thumb | 200px | right| An example of an '''entity tree'''. ]]

All data in LiteMol are organized in a hierarchy represented by the '''entity tree'''. This tree is shown in LiteMol's left panel. When you click on an entity in the tree, you will see all actions applicable to this entity listed in the right panel.

This page lists all types of entities and explains the actions they provide. The entity types can be divided into four sections: Structures, Visualization, Annotations, and Raw Data.

=Structures=

This section describes the entities used for representation of molecular models and electron density maps. It does not contain any information about how these data are visualized.

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set:
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file.
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action.
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.

==Molecule (M)==

A '''Molecule''' entity represents a set of structural data for a '''Molecule''' (which corresponds to one PDB entry or one mmCIF file).

Applicable actions:
* '''Model''' – Creates a model of the molecule ([[LiteMol:Hierarchy#Molecule Model (MM) |Molecule Model]] entity). Some PDB entries (mostly NMR structures) contain multiple models, in such case, the sequential number ('''Index''') of the desired model to be displayed can be specified.
* '''Density Streaming''' - Creates a [[LiteMol:Hierarchy#Density Streaming (BDS) |Density Streaming]] for this molecule. Clicking on an atom or residue in the structure will instantly download and display the density data for the surrounding region. This solution is, in general, much faster than downloading the whole density map (often more than 1 GB). More details are available [http://webchem.ncbr.muni.cz/DensityServer here].
* '''PDBe Validation Report''' – Downloads wwPDB validation data for this molecule from PDBe and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''Ligand Validation Report''' - Downloads validation data for the ligands in this molecule from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB] and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''PDBe Sequence Annotations''' – Downloads sequence annotation data for this molecule from PDBe (collected from sources such as UniProt, InterProt, Pfam etc.) and creates a [[LiteMol:Hierarchy#Sequence Annotations (SA) | Sequence Annotations]] entity.

==Molecule Model (MM)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create an assembly (e.g. a virus capsid). Alternatively, just a part of the model can constitute a relevant assembly (e.g. the model contains a two molecules while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in the crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstrom) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for structures determined by NMR.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. This option is less automatic than '''Macromolecule Visual''' but more flexible. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding volume will be downloaded instantly. This can be useful when a part of the structure has already been downloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains to display the binding site).
* '''Update Model''' – Applicable when multiple models are included in the PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with the specified index (model number). Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model in addition to the current model.

 

==Group (G)==

This type of entity is used to organize multiple entities that are logically connected. For example, a group of selections containing different parts of a model (protein, ligand, and water) or a group of sequence annotations obtained from the same database.

==Molecule Model Selection (SM)==

This is an entity representing a subset of a molecule model. An example is one protein chain, one atom, or a set of all alanine residues. A selection can be created from either a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] entity or a [[LiteMol:Hierarchy#Molecule Visual (VM) | Molecule Visual]] entity. Selections are created using [[LiteMol:SelectionAlgebra | selection algebra language]].

Applicable actions:
* '''Visual''' – Create a visual representation of this selection. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Update Selection''' - Change the name of the [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] or change its definition using [[LiteMol:SelectionAlgebra | selection algebra language]]. (This action may not be not available for automatically generated selections.)

==Density Data (DD)==

Represents a three-dimensional map of electron density (for X-ray crystal structures) or electronic potential maps (for cryo-EM structures). Two types of maps are available for most crystal structures where structure factors are available in the PDB archive: '''2Fo-Fc''' and '''Fo-Fc'''.

Applicable actions:
* '''Surface''' – Creates a visualization of the density isosurface with the defined isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) |Density Visual]] entity).
* '''Interactive Surface''' – Creates a density isosurface which is shown only for a region of the molecule when you click on that region ([[LiteMol:Hierarchy#Interactive Surface (BIS) |Interactive Surface]] entity).
* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.

=Visualization=

This section contains entities that represent different visualizations of molecules and electron density maps.

==Molecule Visual (VM)==

[[File:LiteMol-cartoon.png | thumb | 250px | right| '''Cartoon''' visual for 1CBS. ]]

[[File:LiteMol-CA_trace.png | thumb | 250px | right| '''C-α trace''' visual for 1CBS. ]]

[[File:LiteMol-balls_and_sticks.png | thumb | 250px | right| '''Balls and Sticks''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-VDW_balls.png | thumb | 250px | right| '''VDW Balls''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-surface.png | thumb | 250px | right| '''Surface''' visual for 1CBS. ]]

A '''Molecule Visual''' is simply a visualization of a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] or its part. It is defined mostly by its type and coloring. These can be changed in '''Update Visual''' action. Click on the “+” icon next to “Type” or “Coloring” to modify other attributes. Some attributes are only available for certain types of visualization.

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Update Visual''' – Allows you to change the type of visualization and other attributes.

List of attributes:
* '''Type''' – One of the following:
** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, strands, and unstructured regions.
** '''C-α Trace''' – Simplified wire-like representation of the backbone (no side-chains).
** '''Balls and Sticks''' – Atoms are represented by balls, bonds are shown as sticks connecting them. Keep in mind that most structures from X-ray and cryo-EM experiments do not provide positions of hydrogen atoms, so these are not visible in '''Ball and Sticks''' representation. There are some extra attributes that you can modify:
*** '''VDW''' – Indicates whether all atoms are shown as spheres with uniform radius ('''VDW''' = Off) or the radius of the sphere radius is based on the element's Van der Waals radius ('''VDW''' = On).
*** '''Scale''' – (Only when '''VDW''' = On) The ratio between the sphere radius and the element's Van der Waals radius.
*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the sphere in Angstrom.
*** '''Bond Rds''' – The width (radius) of the sticks.
*** '''Bond''' – Color of the sticks.
** '''VDW Balls''' – Shows atoms as spheres width radii corresponding to their Van der Waals radii.
** '''Surface''' – Shows the smoothed boundary surface of the space “filled” by the molecule. There are some extra attributes that you can modify:
*** '''Probe Radius''' – How much space around an atom is considered as “filled” by this atom.
*** '''Smoothing''' – With lower values, curvature of the surface around individual atoms will be more noticeable. With higher values the surface will be smoother.
*** '''Auto Detail''' - If set to On, the optimal level of detail is automatically derived from the size of the molecule. If set to Off, the level of detail can be adjusted manually (see the next item).
*** '''Detail''' – Defines precisely how the surface should be visualized. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource demanding) when visualizing larger molecules.
*** '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).
* '''Detail''' – Defines how precisely the molecule should be visualized and can range from '''Very Low''' to '''Very High'''. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource demanding) when visualizing larger molecules. If you choose '''Automatic''', LiteMol will infer the optimal level of detail from the molecule's size.
* '''Coloring''' – One of the following:
** '''Chain ID''' – Every chain will be shown in a different color.
** '''Entity ID''' – The same as '''Chain ID''' but chemically identical chains are shown in the same color.
** '''Entity Type''' – Every type of entity (polymer, non-polymer, water) is shown in a different color.
** '''Residue Name''' – A different color is used for each type of residue.
** '''Element Symbol''' – A different color is used for each element.
** '''Rainbow (Chain)''' - Colors each chain in the colors of rainbow from N-terminus (red) to C-terminus (violet) (or from 5' to 3' in nucleic acids).
** '''Rainbow (Entity)''' - Similar to '''Rainbow (Chain)''', but chemically identical chains are treated as a single longer chain (e.g. in a homodimer).
** '''Uniform Color''' – One selected color is used for the whole '''Visual'''.
* '''Highlight''' – The color in which this '''Visual''' will be temporarily colored when hovering over the '''Visual''' entity in the entity tree. When the cursor is placed on an atom or residue, it will be colored in the same way.
* '''Selection''' – If you create a [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] from this '''Visual''', it will be distinguished from the rest of the '''Visual''' by having this color.
* '''Opacity''' – The level of transparency of the '''Visual'''. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).

Please keep in mind that changing the type of a '''Visual''' will in fact remove the current visual and replace it with a new one, so all changes you have applied to the current '''Visual''' (such as creating a selection from it) will be lost! You can go to the superior entity and create a new '''Visual''' besides the current '''Visual'''.

 

==Density Visual (VDD)==

[[File:LiteMol-density_visual.png | thumb | 250px | right| Density isosurface at 1.5 σ (2Fo-Fc). ]]

Represents an isosurface of electron density, i.e. the surface in 3D connecting all the points with the value of electron density equal to a specified isovalue.

Applicable actions:
* '''Update Surface''' – Allows you to change the attributes of the visualization.

List of attributes:
* '''Iso value''' – The isovalue of electron density used for the visualized surface.
* '''Relative''' - Indicates whether normalized ('''Relative''' = On) or unnormalized ('''Relative''' = Off) density values are used. The relationship between the two values is as follows: ''Normalized'' = (''Unnormalized'' - ''Mean'') / ''Sigma''.
* '''Color''' – The color of the surface.
* '''Opacity''' – The level of transparency of the surface. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).
* '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).

 
==Interactive Surface (BIS)==

[[File:LiteMol-interactive_surface.png | thumb | 250px | right| Interactive density isosurface at 1.5 σ (2Fo-Fc) shown for a tryptophan residue and its surroundings with radius 2 Angstroms. ]]

This is a visualization of an isosurface of electron density, just as [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]]. The difference is that this surface is shown only when you click on a residue or an atom in the structure. The surface is shown only for the region around the selected residue or atom. An advantage of this interactive visualization is that the relevant region of density surface is not hindered by the rest of the molecule.

Three default '''Interactive Surfaces''' are created automatically when loading density data: blue surface corresponds to isovalue 1.5 in 2Fo-Fc density map. Green and red surfaces correspond to isovalues +3 and -3 in Fo-Fc difference density maps.

Applicable actions:
* '''Update Interactive Surface''' – Change the attributes of the visualization. These attributes are the same as in the case of [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity. An extra attribute is '''Radius''', which allows you to change the size of the region for which the isosurface is shown. Attribute '''Show''' toggles between interactive visualization around the selected region ('''Show''' = Around Selection) and static visualization of the whole map ('''Show''' = Everything, practically equivalent to [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity).

 

=Annotations=

This section describes entities which can store additional information about the structures, such as validation issues or sequence annotations.

==Validation Report (VR)==

[[File:LiteMol-validation_report.png | thumb | 250px | right| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]

[[File:LiteMol-ligand_validation_report.png | thumb | 250px | right| An oligosaccharide in the structure of ribosome-inactivating protein abrin-a (1ABR) colored by the '''Ligand Validation Report'''. The right-most residue is missing an atom. One of the residues in the center has an atom with which is the chirality. ]]

Represents geometric validation data for this molecule from the wwPDB validation report. The full validation report in PDF can be downloaded from the [http://www.ebi.ac.uk/pdbe/ PDBe site] (find your molecule, click ''Details'' in ''Experiments and Validation'' section, and then ''Full Validation Report'' in the right panel). An example of a validation report is available [http://www.ebi.ac.uk/pdbe/entry-files/download/1rtc_full_validation.pdf here].

Another type of '''Validation Report''' entity is '''Ligand Validation Report''', which represents validation data for the ligands in this structure. These data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB].

Applicable actions:
* '''Apply Coloring''' – The structure will be colored according the validation data. For '''PDBe Validation Report''' the color of each residue depends on the number of geometric outliers it contains: green = 0, yellow = 1, orange = 2, and red = 3 or more. For '''Ligand Validation Report''' the residues with missing atoms are colored in red. Also the atoms with wrong chirality are shown in red (examples can be found in PDB entry 1ABR). Correct residues are shown in green.

 

==Sequence Annotations (SA)==

[[File:LiteMol-annotation.png | thumb | 250px | right| Structure of ricin A chain (4Q2V). The orange color indicates the part annotated as ''Ribosome-inactivating protein, subdomain 1'' by InterPro database. ]]

Represents a collection of sequence annotations via the PDBe API, grouped by the source database.

==Sequence Annotation (SA)==

Represents a single sequence annotation, i.e. assignment of a name to a part of the structure. When you hover above this entity or click on it, the corresponding part of the structure will be shown in a distinctive color.

Applicable actions:
* '''Update PDBe Sequence Annotation''' – Allows you to change the color used for this part of the structure.

 
=Raw Data=

This section contains entities that store data from a file, no matter what these data represent and how their are encoded (i.e. original data from a file before they are parsed). The user will encounter them mostly when loading files from a disk or a URL.

==String Data (SD)==
This entity represents data loaded from a file in textual format (e.g. mmCIF file or PDB file).

Applicable actions:
* '''Molecule''' – Treats the data as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. Make sure to select the appropriate format.
* '''Density Data''' – Treats the data as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity.
* '''CIF Dictionary''' – Treats the data as a CIF dictionary and creates a [[LiteMol:Hierarchy#CIF Dictionary (CD) | CIF Dictionary]] entity. CIF dictionary itself can contain various kinds of data, including molecular structures or density maps.

==Binary Data (BD)==
This entity represents data loaded from a binary file (not human-readable, e.g. [https://github.com/dsehnal/BinaryCIF BinaryCIF] file or CCP4 density file). '''Binary Data''' provides exactly the same actions as [[LiteMol:Hierarchy#String Data (SD) | String Data]].

==CIF Dictionary (CD)==
This entity represents data encoded in a CIF dictionary, which is a flexible format for various kinds of data, so it can contain molecular structures or density maps. A single CIF dictionary can even contain multiple objects (e.g. two density maps: 2Fo-Fc and Fo-Fc).

Applicable actions:
* '''Molecule''' – Treats the data in the '''CIF dictionary''' as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').
* '''Density Data''' – Treats the data in the '''CIF dictionary''' as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').

LiteMol:Hierarchy

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[[File:LiteMol-hierarchy.png | thumb | 200px | right| An example of an '''entity tree'''. ]]

All data in LiteMol are organized in a hierarchy represented by the '''entity tree'''. This tree is shown in LiteMol's left panel. When you click on an entity in the tree, you will see all actions applicable to this entity listed in the right panel.

This page lists all types of entities and explains the actions they provide. The entity types can be divided into four sections: Structures, Visualization, Annotations, and Raw Data.

=Structures=

This section describes the entities used for representation of molecular models and electron density maps. It does not contain any information about how these data are visualized.

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set:
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file.
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action.
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.

==Molecule (M)==

A '''Molecule''' entity represents a set of structural data for a '''Molecule''' (which corresponds to one PDB entry or one mmCIF file).

Applicable actions:
* '''Model''' – Creates a model of the molecule ([[LiteMol:Hierarchy#Molecule Model (MM) |Molecule Model]] entity). Some PDB entries (mostly NMR structures) contain multiple models, in such case, the sequential number ('''Index''') of the desired model to be displayed can be specified.
* '''Density Streaming''' - Creates a [[LiteMol:Hierarchy#Density Streaming (BDS) |Density Streaming]] for this molecule. Clicking on an atom or residue in the structure will instantly download and display the density data for the surrounding region. This solution is, in general, much faster than downloading the whole density map (often more than 1 GB). More details are available [http://webchem.ncbr.muni.cz/DensityServer here].
* '''PDBe Validation Report''' – Downloads wwPDB validation data for this molecule from PDBe and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''Ligand Validation Report''' - Downloads validation data for the ligands in this molecule from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB] and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''PDBe Sequence Annotations''' – Downloads sequence annotation data for this molecule from PDBe (collected from sources such as UniProt, InterProt, Pfam etc.) and creates a [[LiteMol:Hierarchy#Sequence Annotations (SA) | Sequence Annotations]] entity.

==Molecule Model (MM)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create an assembly (e.g. a virus capsid). Alternatively, just a part of the model can constitute a relevant assembly (e.g. the model contains a two molecules while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in the crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstrom) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for structures determined by NMR.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. This option is less automatic than '''Macromolecule Visual''' but more flexible. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding volume will be downloaded instantly. This can be useful when a part of the structure has already been downloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains to display the binding site).
* '''Update Model''' – Applicable when multiple models are included in the PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with the specified index (model number). Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model in addition to the current model.

 

==Group (G)==

This type of entity is used to organize multiple entities that are logically connected. For example, a group of selections containing different parts of a model (protein, ligand, and water) or a group of sequence annotations obtained from the same database.

==Molecule Model Selection (SM)==

This is an entity representing a subset of a molecule model. An example is one protein chain, one atom, or a set of all alanine residues. A selection can be created from either a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] entity or a [[LiteMol:Hierarchy#Molecule Visual (VM) | Molecule Visual]] entity. Selections are created using [[LiteMol:SelectionAlgebra | selection algebra language]].

Applicable actions:
* '''Visual''' – Create a visual representation of this selection. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Update Selection''' - Change the name of the [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] or change its definition using [[LiteMol:SelectionAlgebra | selection algebra language]]. (This action may not be not available for automatically generated selections.)

==Density Data (DD)==

Represents a three-dimensional map of electron density (for X-ray crystal structures) or electronic potential maps (for cryo-EM structures). Two types of maps are available for most crystal structures where structure factors are available in the PDB archive: '''2Fo-Fc''' and '''Fo-Fc'''.

Applicable actions:
* '''Surface''' – Creates a visualization of the density isosurface with the defined isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) |Density Visual]] entity).
* '''Interactive Surface''' – Creates a density isosurface which is shown only for a region of the molecule when you click on that region ([[LiteMol:Hierarchy#Interactive Surface (BIS) |Interactive Surface]] entity).
* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.

=Visualization=

This section contains entities that represent different visualizations of molecules and electron density maps.

==Molecule Visual (VM)==

[[File:LiteMol-cartoon.png | thumb | 250px | right| '''Cartoon''' visual for 1CBS. ]]

[[File:LiteMol-CA_trace.png | thumb | 250px | right| '''C-α trace''' visual for 1CBS. ]]

[[File:LiteMol-balls_and_sticks.png | thumb | 250px | right| '''Balls and Sticks''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-VDW_balls.png | thumb | 250px | right| '''VDW Balls''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-surface.png | thumb | 250px | right| '''Surface''' visual for 1CBS. ]]

A '''Molecule Visual''' is simply a visualization of a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] or its part. It is defined mostly by its type and coloring. These can be changed in '''Update Visual''' action. Click on the “+” icon next to “Type” or “Coloring” to modify other attributes. Some attributes are only available for certain types of visualization.

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Update Visual''' – Allows you to change the type of visualization and other attributes.

List of attributes:
* '''Type''' – One of the following:
** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, strands, and unstructured regions.
** '''C-α Trace''' – Simplified wire-like representation of the backbone (no side-chains).
** '''Balls and Sticks''' – Atoms are represented by balls, bonds are shown as sticks connecting them. Keep in mind that most structures from X-ray and cryo-EM experiments do not provide positions of hydrogen atoms, so these are not visible in '''Ball and Sticks''' representation. There are some extra attributes that you can modify:
*** '''VDW''' – Indicates whether all atoms are shown as spheres with uniform radius ('''VDW''' = Off) or the radius of the sphere radius is based on the element's Van der Waals radius ('''VDW''' = On).
*** '''Scale''' – (Only when '''VDW''' = On) The ratio between the sphere radius and the element's Van der Waals radius.
*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the sphere in Angstrom.
*** '''Bond Rds''' – The width (radius) of the sticks.
*** '''Bond''' – Color of the sticks.
** '''VDW Balls''' – Shows atoms as spheres width radii corresponding to their Van der Waals radii.
** '''Surface''' – Shows the smoothed boundary surface of the space “filled” by the molecule. There are some extra attributes that you can modify:
*** '''Probe Radius''' – How much space around an atom is considered as “filled” by this atom.
*** '''Smoothing''' – With lower values, curvature of the surface around individual atoms will be more noticeable. With higher values the surface will be smoother.
*** '''Auto Detail''' - If set to On, the optimal level of detail is automatically derived from the size of the molecule. If set to Off, the level of detail can be adjusted manually (see the next item).
*** '''Detail''' – Defines precisely how the surface should be visualized. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource demanding) when visualizing larger molecules.
*** '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).
* '''Detail''' – Defines how precisely the molecule should be visualized and can range from '''Very Low''' to '''Very High'''. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource demanding) when visualizing larger molecules. If you choose '''Automatic''', LiteMol will infer the optimal level of detail from the molecule's size.
* '''Coloring''' – One of the following:
** '''Chain ID''' – Every chain will be shown in a different color.
** '''Entity ID''' – The same as '''Chain ID''' but chemically identical chains are shown in the same color.
** '''Entity Type''' – Every type of entity (polymer, non-polymer, water) is shown in a different color.
** '''Residue Name''' – A different color is used for each type of residue.
** '''Element Symbol''' – A different color is used for each element.
** '''Rainbow (Chain)''' - Colors each chain in the colors of rainbow from N-terminus (red) to C-terminus (violet) (or from 5' to 3' in nucleic acids).
** '''Rainbow (Entity)''' - Similar to '''Rainbow (Chain)''', but chemically identical chains are treated as a single longer chain (e.g. in a homodimer).
** '''Uniform Color''' – One selected color is used for the whole '''Visual'''.
* '''Highlight''' – The color in which this '''Visual''' will be temporarily colored when hovering over the '''Visual''' entity in the entity tree. When the cursor is placed on an atom or residue, it will be colored in the same way.
* '''Selection''' – If you create a [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] from this '''Visual''', it will be distinguished from the rest of the '''Visual''' by having this color.
* '''Opacity''' – The level of transparency of the '''Visual'''. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).

Please keep in mind that changing the type of a '''Visual''' will in fact remove the current visual and replace it with a new one, so all changes you have applied to the current '''Visual''' (such as creating a selection from it) will be lost! You can go to the superior entity and create a new '''Visual''' besides the current '''Visual'''.

 

==Density Visual (VDD)==

[[File:LiteMol-density_visual.png | thumb | 250px | right| Density isosurface at 1.5 σ (2Fo-Fc). ]]

Represents an isosurface of electron density, i.e. the surface in 3D connecting all the points with the value of electron density equal to a specified isovalue.

Applicable actions:
* '''Update Surface''' – Allows you to change the attributes of the visualization.

List of attributes:
* '''Iso value''' – The isovalue of electron density used for the visualized surface.
* '''Relative''' - Indicates whether normalized ('''Relative''' = On) or unnormalized ('''Relative''' = Off) density values are used. The relationship between the two values is as follows: ''Normalized'' = (''Unnormalized'' - ''Mean'') / ''Sigma''.
* '''Color''' – The color of the surface.
* '''Opacity''' – The level of transparency of the surface. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).
* '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).

 
==Interactive Surface (BIS)==

[[File:LiteMol-interactive_surface.png | thumb | 250px | right| Interactive density isosurface at 1.5 σ (2Fo-Fc) shown for a tryptophan residue and its surroundings with radius 2 Angstroms. ]]

This is a visualization of an isosurface of electron density, just as [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]]. The difference is that this surface is shown only when you click on a residue or an atom in the structure. The surface is shown only for the region around the selected residue or atom. An advantage of this interactive visualization is that the relevant region of density surface is not hindered by the rest of the molecule.

Three default '''Interactive Surfaces''' are created automatically when loading density data: blue surface corresponds to isovalue 1.5 in 2Fo-Fc density map. Green and red surfaces correspond to isovalues +3 and -3 in Fo-Fc difference density maps.

Applicable actions:
* '''Update Interactive Surface''' – Change the attributes of the visualization. These attributes are the same as in the case of [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity. An extra attribute is '''Radius''', which allows you to change the size of the region for which the isosurface is shown. Attribute '''Show''' toggles between interactive visualization around the selected region ('''Show''' = Around Selection) and static visualization of the whole map ('''Show''' = Everything, practically equivalent to [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity).

 

=Annotations=

This section describes entities which can store additional information about the structures, such as validation issues or sequence annotations.

==Validation Report (VR)==

[[File:LiteMol-validation_report.png | thumb | 250px | right| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]

[[File:LiteMol-ligand_validation_report.png | thumb | 250px | right| An oligosaccharide in the structure of ribosome-inactivating protein abrin-a (1ABR) colored by the '''Ligand Validation Report'''. The right-most residue is missing an atom. One of the residues in the center has an atom with which is the chirality. ]]

Represents geometric validation data for this molecule from the wwPDB validation report. The full validation report in PDF can be downloaded from the [http://www.ebi.ac.uk/pdbe/ PDBe site] (find your molecule, click ''Details'' in ''Experiments and Validation'' section, and then ''Full Validation Report'' in the right panel). An example of a validation report is available [http://www.ebi.ac.uk/pdbe/entry-files/download/1rtc_full_validation.pdf here].

Another type of '''Validation Report''' entity is '''Ligand Validation Report''', which represents validation data for the ligands in this structure. These data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB].

Applicable actions:
* '''Apply Coloring''' – The structure will be colored according the validation data. For '''PDBe Validation Report''' the color of each residue depends on the number of geometric outliers it contains: green = 0, yellow = 1, orange = 2, and red = 3 or more. For '''Ligand Validation Report''' the residues with missing atoms are colored in red. Also the atoms with wrong chirality are shown in red (examples can be found in PDB entry 1ABR). Correct residues are shown in green.

 

==Sequence Annotations (SA)==

[[File:LiteMol-annotation.png | thumb | 250px | right| Structure of ricin A chain (4Q2V). The orange color indicates the part annotated as ''Ribosome-inactivating protein, subdomain 1'' by InterPro database. ]]

Represents a collection of sequence annotations from PDBe, grouped by the source database.

==Sequence Annotation (SA)==

Represents a single sequence annotation, i.e. assignment of a name to a part of the structure. When you hover above this entity or click on it, the corresponding part of the structure will be shown in a distinctive color.

Applicable actions:
* '''Update PDBe Sequence Annotation''' – Allows you to change the color used for this part of the structure.

 
=Raw Data=

This section contains entities that store data from a file, no matter what these data represent and how their are encoded (i.e. original data from a file before they are parsed). The user will encounter them mostly when loading files from a disk or a URL.

==String Data (SD)==
This entity represents data loaded from a file in textual format (e.g. mmCIF file or PDB file).

Applicable actions:
* '''Molecule''' – Treats the data as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. Make sure to select the appropriate format.
* '''Density Data''' – Treats the data as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity.
* '''CIF Dictionary''' – Treats the data as a CIF dictionary and creates a [[LiteMol:Hierarchy#CIF Dictionary (CD) | CIF Dictionary]] entity. CIF dictionary itself can contain various kinds of data, including molecular structures or density maps.

==Binary Data (BD)==
This entity represents data loaded from a binary file (not human-readable, e.g. [https://github.com/dsehnal/BinaryCIF BinaryCIF] file or CCP4 density file). '''Binary Data''' provides exactly the same actions as [[LiteMol:Hierarchy#String Data (SD) | String Data]].

==CIF Dictionary (CD)==
This entity represents data encoded in a CIF dictionary, which is a flexible format for various kinds of data, so it can contain molecular structures or density maps. A single CIF dictionary can even contain multiple objects (e.g. two density maps: 2Fo-Fc and Fo-Fc).

Applicable actions:
* '''Molecule''' – Treats the data in the '''CIF dictionary''' as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').
* '''Density Data''' – Treats the data in the '''CIF dictionary''' as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').

LiteMol:Hierarchy

2017-05-05T11:52:39Z

Matthew: /* Interactive Surface (BIS) */ mjc edit

[[File:LiteMol-hierarchy.png | thumb | 200px | right| An example of an '''entity tree'''. ]]

All data in LiteMol are organized in a hierarchy represented by the '''entity tree'''. This tree is shown in LiteMol's left panel. When you click on an entity in the tree, you will see all actions applicable to this entity listed in the right panel.

This page lists all types of entities and explains the actions they provide. The entity types can be divided into four sections: Structures, Visualization, Annotations, and Raw Data.

=Structures=

This section describes the entities used for representation of molecular models and electron density maps. It does not contain any information about how these data are visualized.

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set:
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file.
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action.
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.

==Molecule (M)==

A '''Molecule''' entity represents a set of structural data for a '''Molecule''' (which corresponds to one PDB entry or one mmCIF file).

Applicable actions:
* '''Model''' – Creates a model of the molecule ([[LiteMol:Hierarchy#Molecule Model (MM) |Molecule Model]] entity). Some PDB entries (mostly NMR structures) contain multiple models, in such case, the sequential number ('''Index''') of the desired model to be displayed can be specified.
* '''Density Streaming''' - Creates a [[LiteMol:Hierarchy#Density Streaming (BDS) |Density Streaming]] for this molecule. Clicking on an atom or residue in the structure will instantly download and display the density data for the surrounding region. This solution is, in general, much faster than downloading the whole density map (often more than 1 GB). More details are available [http://webchem.ncbr.muni.cz/DensityServer here].
* '''PDBe Validation Report''' – Downloads wwPDB validation data for this molecule from PDBe and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''Ligand Validation Report''' - Downloads validation data for the ligands in this molecule from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB] and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''PDBe Sequence Annotations''' – Downloads sequence annotation data for this molecule from PDBe (collected from sources such as UniProt, InterProt, Pfam etc.) and creates a [[LiteMol:Hierarchy#Sequence Annotations (SA) | Sequence Annotations]] entity.

==Molecule Model (MM)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create an assembly (e.g. a virus capsid). Alternatively, just a part of the model can constitute a relevant assembly (e.g. the model contains a two molecules while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in the crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstrom) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for structures determined by NMR.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. This option is less automatic than '''Macromolecule Visual''' but more flexible. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding volume will be downloaded instantly. This can be useful when a part of the structure has already been downloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains to display the binding site).
* '''Update Model''' – Applicable when multiple models are included in the PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with the specified index (model number). Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model in addition to the current model.

 

==Group (G)==

This type of entity is used to organize multiple entities that are logically connected. For example, a group of selections containing different parts of a model (protein, ligand, and water) or a group of sequence annotations obtained from the same database.

==Molecule Model Selection (SM)==

This is an entity representing a subset of a molecule model. An example is one protein chain, one atom, or a set of all alanine residues. A selection can be created from either a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] entity or a [[LiteMol:Hierarchy#Molecule Visual (VM) | Molecule Visual]] entity. Selections are created using [[LiteMol:SelectionAlgebra | selection algebra language]].

Applicable actions:
* '''Visual''' – Create a visual representation of this selection. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Update Selection''' - Change the name of the [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] or change its definition using [[LiteMol:SelectionAlgebra | selection algebra language]]. (This action may not be not available for automatically generated selections.)

==Density Data (DD)==

Represents a three-dimensional map of electron density (for X-ray crystal structures) or electronic potential maps (for cryo-EM structures). Two types of maps are available for most crystal structures where structure factors are available in the PDB archive: '''2Fo-Fc''' and '''Fo-Fc'''.

Applicable actions:
* '''Surface''' – Creates a visualization of the density isosurface with the defined isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) |Density Visual]] entity).
* '''Interactive Surface''' – Creates a density isosurface which is shown only for a region of the molecule when you click on that region ([[LiteMol:Hierarchy#Interactive Surface (BIS) |Interactive Surface]] entity).
* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.

=Visualization=

This section contains entities that represent different visualizations of molecules and electron density maps.

==Molecule Visual (VM)==

[[File:LiteMol-cartoon.png | thumb | 250px | right| '''Cartoon''' visual for 1CBS. ]]

[[File:LiteMol-CA_trace.png | thumb | 250px | right| '''C-α trace''' visual for 1CBS. ]]

[[File:LiteMol-balls_and_sticks.png | thumb | 250px | right| '''Balls and Sticks''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-VDW_balls.png | thumb | 250px | right| '''VDW Balls''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-surface.png | thumb | 250px | right| '''Surface''' visual for 1CBS. ]]

A '''Molecule Visual''' is simply a visualization of a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] or its part. It is defined mostly by its type and coloring. These can be changed in '''Update Visual''' action. Click on the “+” icon next to “Type” or “Coloring” to modify other attributes. Some attributes are only available for certain types of visualization.

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Update Visual''' – Allows you to change the type of visualization and other attributes.

List of attributes:
* '''Type''' – One of the following:
** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, strands, and unstructured regions.
** '''C-α Trace''' – Simplified wire-like representation of the backbone (no side-chains).
** '''Balls and Sticks''' – Atoms are represented by balls, bonds are shown as sticks connecting them. Keep in mind that most structures from X-ray and cryo-EM experiments do not provide positions of hydrogen atoms, so these are not visible in '''Ball and Sticks''' representation. There are some extra attributes that you can modify:
*** '''VDW''' – Indicates whether all atoms are shown as spheres with uniform radius ('''VDW''' = Off) or the radius of the sphere radius is based on the element's Van der Waals radius ('''VDW''' = On).
*** '''Scale''' – (Only when '''VDW''' = On) The ratio between the sphere radius and the element's Van der Waals radius.
*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the sphere in Angstrom.
*** '''Bond Rds''' – The width (radius) of the sticks.
*** '''Bond''' – Color of the sticks.
** '''VDW Balls''' – Shows atoms as spheres width radii corresponding to their Van der Waals radii.
** '''Surface''' – Shows the smoothed boundary surface of the space “filled” by the molecule. There are some extra attributes that you can modify:
*** '''Probe Radius''' – How much space around an atom is considered as “filled” by this atom.
*** '''Smoothing''' – With lower values, curvature of the surface around individual atoms will be more noticeable. With higher values the surface will be smoother.
*** '''Auto Detail''' - If set to On, the optimal level of detail is automatically derived from the size of the molecule. If set to Off, the level of detail can be adjusted manually (see the next item).
*** '''Detail''' – Defines precisely how the surface should be visualized. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource demanding) when visualizing larger molecules.
*** '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).
* '''Detail''' – Defines how precisely the molecule should be visualized and can range from '''Very Low''' to '''Very High'''. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource demanding) when visualizing larger molecules. If you choose '''Automatic''', LiteMol will infer the optimal level of detail from the molecule's size.
* '''Coloring''' – One of the following:
** '''Chain ID''' – Every chain will be shown in a different color.
** '''Entity ID''' – The same as '''Chain ID''' but chemically identical chains are shown in the same color.
** '''Entity Type''' – Every type of entity (polymer, non-polymer, water) is shown in a different color.
** '''Residue Name''' – A different color is used for each type of residue.
** '''Element Symbol''' – A different color is used for each element.
** '''Rainbow (Chain)''' - Colors each chain in the colors of rainbow from N-terminus (red) to C-terminus (violet) (or from 5' to 3' in nucleic acids).
** '''Rainbow (Entity)''' - Similar to '''Rainbow (Chain)''', but chemically identical chains are treated as a single longer chain (e.g. in a homodimer).
** '''Uniform Color''' – One selected color is used for the whole '''Visual'''.
* '''Highlight''' – The color in which this '''Visual''' will be temporarily colored when hovering over the '''Visual''' entity in the entity tree. When the cursor is placed on an atom or residue, it will be colored in the same way.
* '''Selection''' – If you create a [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] from this '''Visual''', it will be distinguished from the rest of the '''Visual''' by having this color.
* '''Opacity''' – The level of transparency of the '''Visual'''. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).

Please keep in mind that changing the type of a '''Visual''' will in fact remove the current visual and replace it with a new one, so all changes you have applied to the current '''Visual''' (such as creating a selection from it) will be lost! You can go to the superior entity and create a new '''Visual''' besides the current '''Visual'''.

 

==Density Visual (VDD)==

[[File:LiteMol-density_visual.png | thumb | 250px | right| Density isosurface at 1.5 σ (2Fo-Fc). ]]

Represents an isosurface of electron density, i.e. the surface in 3D connecting all the points with the value of electron density equal to a specified isovalue.

Applicable actions:
* '''Update Surface''' – Allows you to change the attributes of the visualization.

List of attributes:
* '''Iso value''' – The isovalue of electron density used for the visualized surface.
* '''Relative''' - Indicates whether normalized ('''Relative''' = On) or unnormalized ('''Relative''' = Off) density values are used. The relationship between the two values is as follows: ''Normalized'' = (''Unnormalized'' - ''Mean'') / ''Sigma''.
* '''Color''' – The color of the surface.
* '''Opacity''' – The level of transparency of the surface. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).
* '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).

 
==Interactive Surface (BIS)==

[[File:LiteMol-interactive_surface.png | thumb | 250px | right| Interactive density isosurface at 1.5 σ (2Fo-Fc) shown for a tryptophan residue and its surroundings with radius 2 Angstroms. ]]

This is a visualization of an isosurface of electron density, just as [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]]. The difference is that this surface is shown only when you click on a residue or an atom in the structure. The surface is shown only for the region around the selected residue or atom. An advantage of this interactive visualization is that the relevant region of density surface is not hindered by the rest of the molecule.

Three default '''Interactive Surfaces''' are created automatically when loading density data: blue surface corresponds to isovalue 1.5 in 2Fo-Fc density map. Green and red surfaces correspond to isovalues +3 and -3 in Fo-Fc difference density maps.

Applicable actions:
* '''Update Interactive Surface''' – Change the attributes of the visualization. These attributes are the same as in the case of [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity. An extra attribute is '''Radius''', which allows you to change the size of the region for which the isosurface is shown. Attribute '''Show''' toggles between interactive visualization around the selected region ('''Show''' = Around Selection) and static visualization of the whole map ('''Show''' = Everything, practically equivalent to [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity).

 

=Annotations=

This section describes entities which can store additional information about the structures, such as validation issues or sequence annotations.

==Validation Report (VR)==

[[File:LiteMol-validation_report.png | thumb | 250px | right| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]

[[File:LiteMol-ligand_validation_report.png | thumb | 250px | right| An oligosaccharide in the structure of ribosom-inactivating protein abrin-a (1ABR) colored by the '''Ligand Validation Report'''. The right-most residue is missing an atom. One of the residues in the center has an atom with wrongly annotated chirality. ]]

Represents validation data for this molecule from PDBe. The full validation report in PDF can be downloaded from the [http://www.ebi.ac.uk/pdbe/ PDBe site] (find your molecule, click ''Details'' in ''Experiments and Validation'' section, and then ''Full Validation Report'' in the right panel). An example of a validation report is available [http://www.ebi.ac.uk/pdbe/entry-files/download/1rtc_full_validation.pdf here].

Another type of '''Validation Report''' entity is '''Ligand Validation Report''', which represents validation data for the ligands in this molecule. This data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB].

Applicable actions:
* '''Apply Coloring''' – The structure will be colored according the validation data. For '''PDBe Validation Report''' the color of each residue depends on the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2, and red = 3 or more. For '''Ligand Validation Report''' the residues with missing atoms are colored in red. Also the atoms with wrong chirality are shown in red (examples can be found in PDB entry 1ABR). The correct residues are shown in green.

 
==Sequence Annotations (SA)==

[[File:LiteMol-annotation.png | thumb | 250px | right| Structure of ricin A chain (4Q2V). The orange color indicates the part annotated as ''Ribosome-inactivating protein, subdomain 1'' by InterPro database. ]]

Represents a collection of sequence annotations from PDBe, grouped by the source database.

==Sequence Annotation (SA)==

Represents a single sequence annotation, i.e. assignment of a name to a part of the structure. When you hover above this entity or click on it, the corresponding part of the structure will be shown in a distinctive color.

Applicable actions:
* '''Update PDBe Sequence Annotation''' – Allows you to change the color used for this part of the structure.

 
=Raw Data=

This section contains entities that store data from a file, no matter what these data represent and how their are encoded (i.e. original data from a file before they are parsed). The user will encounter them mostly when loading files from a disk or a URL.

==String Data (SD)==
This entity represents data loaded from a file in textual format (e.g. mmCIF file or PDB file).

Applicable actions:
* '''Molecule''' – Treats the data as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. Make sure to select the appropriate format.
* '''Density Data''' – Treats the data as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity.
* '''CIF Dictionary''' – Treats the data as a CIF dictionary and creates a [[LiteMol:Hierarchy#CIF Dictionary (CD) | CIF Dictionary]] entity. CIF dictionary itself can contain various kinds of data, including molecular structures or density maps.

==Binary Data (BD)==
This entity represents data loaded from a binary file (not human-readable, e.g. [https://github.com/dsehnal/BinaryCIF BinaryCIF] file or CCP4 density file). '''Binary Data''' provides exactly the same actions as [[LiteMol:Hierarchy#String Data (SD) | String Data]].

==CIF Dictionary (CD)==
This entity represents data encoded in a CIF dictionary, which is a flexible format for various kinds of data, so it can contain molecular structures or density maps. A single CIF dictionary can even contain multiple objects (e.g. two density maps: 2Fo-Fc and Fo-Fc).

Applicable actions:
* '''Molecule''' – Treats the data in the '''CIF dictionary''' as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').
* '''Density Data''' – Treats the data in the '''CIF dictionary''' as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').

LiteMol:Hierarchy

2017-05-05T10:57:04Z

Matthew: /* Molecule Visual (VM) */ mjc edit

[[File:LiteMol-hierarchy.png | thumb | 200px | right| An example of an '''entity tree'''. ]]

All data in LiteMol are organized in a hierarchy represented by the '''entity tree'''. This tree is shown in LiteMol's left panel. When you click on an entity in the tree, you will see all actions applicable to this entity listed in the right panel.

This page lists all types of entities and explains the actions they provide. The entity types can be divided into four sections: Structures, Visualization, Annotations, and Raw Data.

=Structures=

This section describes the entities used for representation of molecular models and electron density maps. It does not contain any information about how these data are visualized.

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set:
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file.
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action.
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.

==Molecule (M)==

A '''Molecule''' entity represents a set of structural data for a '''Molecule''' (which corresponds to one PDB entry or one mmCIF file).

Applicable actions:
* '''Model''' – Creates a model of the molecule ([[LiteMol:Hierarchy#Molecule Model (MM) |Molecule Model]] entity). Some PDB entries (mostly NMR structures) contain multiple models, in such case, the sequential number ('''Index''') of the desired model to be displayed can be specified.
* '''Density Streaming''' - Creates a [[LiteMol:Hierarchy#Density Streaming (BDS) |Density Streaming]] for this molecule. Clicking on an atom or residue in the structure will instantly download and display the density data for the surrounding region. This solution is, in general, much faster than downloading the whole density map (often more than 1 GB). More details are available [http://webchem.ncbr.muni.cz/DensityServer here].
* '''PDBe Validation Report''' – Downloads wwPDB validation data for this molecule from PDBe and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''Ligand Validation Report''' - Downloads validation data for the ligands in this molecule from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB] and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''PDBe Sequence Annotations''' – Downloads sequence annotation data for this molecule from PDBe (collected from sources such as UniProt, InterProt, Pfam etc.) and creates a [[LiteMol:Hierarchy#Sequence Annotations (SA) | Sequence Annotations]] entity.

==Molecule Model (MM)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create an assembly (e.g. a virus capsid). Alternatively, just a part of the model can constitute a relevant assembly (e.g. the model contains a two molecules while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in the crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstrom) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for structures determined by NMR.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. This option is less automatic than '''Macromolecule Visual''' but more flexible. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding volume will be downloaded instantly. This can be useful when a part of the structure has already been downloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains to display the binding site).
* '''Update Model''' – Applicable when multiple models are included in the PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with the specified index (model number). Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model in addition to the current model.

 

==Group (G)==

This type of entity is used to organize multiple entities that are logically connected. For example, a group of selections containing different parts of a model (protein, ligand, and water) or a group of sequence annotations obtained from the same database.

==Molecule Model Selection (SM)==

This is an entity representing a subset of a molecule model. An example is one protein chain, one atom, or a set of all alanine residues. A selection can be created from either a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] entity or a [[LiteMol:Hierarchy#Molecule Visual (VM) | Molecule Visual]] entity. Selections are created using [[LiteMol:SelectionAlgebra | selection algebra language]].

Applicable actions:
* '''Visual''' – Create a visual representation of this selection. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Update Selection''' - Change the name of the [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] or change its definition using [[LiteMol:SelectionAlgebra | selection algebra language]]. (This action may not be not available for automatically generated selections.)

==Density Data (DD)==

Represents a three-dimensional map of electron density (for X-ray crystal structures) or electronic potential maps (for cryo-EM structures). Two types of maps are available for most crystal structures where structure factors are available in the PDB archive: '''2Fo-Fc''' and '''Fo-Fc'''.

Applicable actions:
* '''Surface''' – Creates a visualization of the density isosurface with the defined isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) |Density Visual]] entity).
* '''Interactive Surface''' – Creates a density isosurface which is shown only for a region of the molecule when you click on that region ([[LiteMol:Hierarchy#Interactive Surface (BIS) |Interactive Surface]] entity).
* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.

=Visualization=

This section contains entities that represent different visualizations of molecules and electron density maps.

==Molecule Visual (VM)==

[[File:LiteMol-cartoon.png | thumb | 250px | right| '''Cartoon''' visual for 1CBS. ]]

[[File:LiteMol-CA_trace.png | thumb | 250px | right| '''C-α trace''' visual for 1CBS. ]]

[[File:LiteMol-balls_and_sticks.png | thumb | 250px | right| '''Balls and Sticks''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-VDW_balls.png | thumb | 250px | right| '''VDW Balls''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-surface.png | thumb | 250px | right| '''Surface''' visual for 1CBS. ]]

A '''Molecule Visual''' is simply a visualization of a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] or its part. It is defined mostly by its type and coloring. These can be changed in '''Update Visual''' action. Click on the “+” icon next to “Type” or “Coloring” to modify other attributes. Some attributes are only available for certain types of visualization.

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Update Visual''' – Allows you to change the type of visualization and other attributes.

List of attributes:
* '''Type''' – One of the following:
** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, strands, and unstructured regions.
** '''C-α Trace''' – Simplified wire-like representation of the backbone (no side-chains).
** '''Balls and Sticks''' – Atoms are represented by balls, bonds are shown as sticks connecting them. Keep in mind that most structures from X-ray and cryo-EM experiments do not provide positions of hydrogen atoms, so these are not visible in '''Ball and Sticks''' representation. There are some extra attributes that you can modify:
*** '''VDW''' – Indicates whether all atoms are shown as spheres with uniform radius ('''VDW''' = Off) or the radius of the sphere radius is based on the element's Van der Waals radius ('''VDW''' = On).
*** '''Scale''' – (Only when '''VDW''' = On) The ratio between the sphere radius and the element's Van der Waals radius.
*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the sphere in Angstrom.
*** '''Bond Rds''' – The width (radius) of the sticks.
*** '''Bond''' – Color of the sticks.
** '''VDW Balls''' – Shows atoms as spheres width radii corresponding to their Van der Waals radii.
** '''Surface''' – Shows the smoothed boundary surface of the space “filled” by the molecule. There are some extra attributes that you can modify:
*** '''Probe Radius''' – How much space around an atom is considered as “filled” by this atom.
*** '''Smoothing''' – With lower values, curvature of the surface around individual atoms will be more noticeable. With higher values the surface will be smoother.
*** '''Auto Detail''' - If set to On, the optimal level of detail is automatically derived from the size of the molecule. If set to Off, the level of detail can be adjusted manually (see the next item).
*** '''Detail''' – Defines precisely how the surface should be visualized. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource demanding) when visualizing larger molecules.
*** '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).
* '''Detail''' – Defines how precisely the molecule should be visualized and can range from '''Very Low''' to '''Very High'''. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource demanding) when visualizing larger molecules. If you choose '''Automatic''', LiteMol will infer the optimal level of detail from the molecule's size.
* '''Coloring''' – One of the following:
** '''Chain ID''' – Every chain will be shown in a different color.
** '''Entity ID''' – The same as '''Chain ID''' but chemically identical chains are shown in the same color.
** '''Entity Type''' – Every type of entity (polymer, non-polymer, water) is shown in a different color.
** '''Residue Name''' – A different color is used for each type of residue.
** '''Element Symbol''' – A different color is used for each element.
** '''Rainbow (Chain)''' - Colors each chain in the colors of rainbow from N-terminus (red) to C-terminus (violet) (or from 5' to 3' in nucleic acids).
** '''Rainbow (Entity)''' - Similar to '''Rainbow (Chain)''', but chemically identical chains are treated as a single longer chain (e.g. in a homodimer).
** '''Uniform Color''' – One selected color is used for the whole '''Visual'''.
* '''Highlight''' – The color in which this '''Visual''' will be temporarily colored when hovering over the '''Visual''' entity in the entity tree. When the cursor is placed on an atom or residue, it will be colored in the same way.
* '''Selection''' – If you create a [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] from this '''Visual''', it will be distinguished from the rest of the '''Visual''' by having this color.
* '''Opacity''' – The level of transparency of the '''Visual'''. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).

Please keep in mind that changing the type of a '''Visual''' will in fact remove the current visual and replace it with a new one, so all changes you have applied to the current '''Visual''' (such as creating a selection from it) will be lost! You can go to the superior entity and create a new '''Visual''' besides the current '''Visual'''.

 

==Density Visual (VDD)==

[[File:LiteMol-density_visual.png | thumb | 250px | right| Density isosurface at 1.5 σ (2Fo-Fc). ]]

Represents an isosurface of electron density, i.e. the surface in 3D connecting all the points with the value of electron density equal to a specified isovalue.

Applicable actions:
* '''Update Surface''' – Allows you to change the attributes of the visualization.

List of attributes:
* '''Iso value''' – The isovalue of electron density used for the visualized surface.
* '''Relative''' - Indicates whether normalized ('''Relative''' = On) or unnormalized ('''Relative''' = Off) density values are used. The relationship between the two values is as follows: ''Normalized'' = (''Unnormalized'' - ''Mean'') / ''Sigma''.
* '''Color''' – The color of the surface.
* '''Opacity''' – The level of transparency of the surface. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).
* '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).

 
==Interactive Surface (BIS)==

[[File:LiteMol-interactive_surface.png | thumb | 250px | right| Interactive density isosurface at 1.5 σ (2Fo-Fc) shown for a tryptophan residue and its surroundings with radius 2 Angstroms. ]]

This is a visualization of an isosurface of electron density, just as [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]]. The difference is that this surface is shown only when you click on a residue or an atom in the structure. The surface is shown only for the region around the selected residue or atom. An advantage of this interactive visualization is that the relevant region of density surface is not hindered by the rest of the molecule.

Three default '''Interactive Surfaces''' are created automatically when loading density data: blue surface corresponds to isovalue 1.5 in 2Fo-Fc density map. Green and red surfaces correspond to isovalues +3 and -3 in Fo-Fc density map.

Applicable actions:
* '''Update Interactive Surface''' – Change the attributes of the visualization. These attributes are the same as in the case of [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity. An extra attribute is '''Radius''', which allows you to change the size of the region for which the isosurface is shown. Attribute '''Show''' toggles between interactive visualization around the selected region ('''Show''' = Around Selection) and static visualization of the whole map ('''Show''' = Everything, practically equivalent to [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity).

 
=Annotations=

This section describes entities which can store additional information about the structures, such as validation issues or sequence annotations.

==Validation Report (VR)==

[[File:LiteMol-validation_report.png | thumb | 250px | right| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]

[[File:LiteMol-ligand_validation_report.png | thumb | 250px | right| An oligosaccharide in the structure of ribosom-inactivating protein abrin-a (1ABR) colored by the '''Ligand Validation Report'''. The right-most residue is missing an atom. One of the residues in the center has an atom with wrongly annotated chirality. ]]

Represents validation data for this molecule from PDBe. The full validation report in PDF can be downloaded from the [http://www.ebi.ac.uk/pdbe/ PDBe site] (find your molecule, click ''Details'' in ''Experiments and Validation'' section, and then ''Full Validation Report'' in the right panel). An example of a validation report is available [http://www.ebi.ac.uk/pdbe/entry-files/download/1rtc_full_validation.pdf here].

Another type of '''Validation Report''' entity is '''Ligand Validation Report''', which represents validation data for the ligands in this molecule. This data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB].

Applicable actions:
* '''Apply Coloring''' – The structure will be colored according the validation data. For '''PDBe Validation Report''' the color of each residue depends on the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2, and red = 3 or more. For '''Ligand Validation Report''' the residues with missing atoms are colored in red. Also the atoms with wrong chirality are shown in red (examples can be found in PDB entry 1ABR). The correct residues are shown in green.

 
==Sequence Annotations (SA)==

[[File:LiteMol-annotation.png | thumb | 250px | right| Structure of ricin A chain (4Q2V). The orange color indicates the part annotated as ''Ribosome-inactivating protein, subdomain 1'' by InterPro database. ]]

Represents a collection of sequence annotations from PDBe, grouped by the source database.

==Sequence Annotation (SA)==

Represents a single sequence annotation, i.e. assignment of a name to a part of the structure. When you hover above this entity or click on it, the corresponding part of the structure will be shown in a distinctive color.

Applicable actions:
* '''Update PDBe Sequence Annotation''' – Allows you to change the color used for this part of the structure.

 
=Raw Data=

This section contains entities that store data from a file, no matter what these data represent and how their are encoded (i.e. original data from a file before they are parsed). The user will encounter them mostly when loading files from a disk or a URL.

==String Data (SD)==
This entity represents data loaded from a file in textual format (e.g. mmCIF file or PDB file).

Applicable actions:
* '''Molecule''' – Treats the data as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. Make sure to select the appropriate format.
* '''Density Data''' – Treats the data as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity.
* '''CIF Dictionary''' – Treats the data as a CIF dictionary and creates a [[LiteMol:Hierarchy#CIF Dictionary (CD) | CIF Dictionary]] entity. CIF dictionary itself can contain various kinds of data, including molecular structures or density maps.

==Binary Data (BD)==
This entity represents data loaded from a binary file (not human-readable, e.g. [https://github.com/dsehnal/BinaryCIF BinaryCIF] file or CCP4 density file). '''Binary Data''' provides exactly the same actions as [[LiteMol:Hierarchy#String Data (SD) | String Data]].

==CIF Dictionary (CD)==
This entity represents data encoded in a CIF dictionary, which is a flexible format for various kinds of data, so it can contain molecular structures or density maps. A single CIF dictionary can even contain multiple objects (e.g. two density maps: 2Fo-Fc and Fo-Fc).

Applicable actions:
* '''Molecule''' – Treats the data in the '''CIF dictionary''' as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').
* '''Density Data''' – Treats the data in the '''CIF dictionary''' as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').

LiteMol:Hierarchy

2017-05-05T10:01:39Z

Matthew: /* Density Data (DD) */ mjc edit

[[File:LiteMol-hierarchy.png | thumb | 200px | right| An example of an '''entity tree'''. ]]

All data in LiteMol are organized in a hierarchy represented by the '''entity tree'''. This tree is shown in LiteMol's left panel. When you click on an entity in the tree, you will see all actions applicable to this entity listed in the right panel.

This page lists all types of entities and explains the actions they provide. The entity types can be divided into four sections: Structures, Visualization, Annotations, and Raw Data.

=Structures=

This section describes the entities used for representation of molecular models and electron density maps. It does not contain any information about how these data are visualized.

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set:
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file.
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action.
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.

==Molecule (M)==

A '''Molecule''' entity represents a set of structural data for a '''Molecule''' (which corresponds to one PDB entry or one mmCIF file).

Applicable actions:
* '''Model''' – Creates a model of the molecule ([[LiteMol:Hierarchy#Molecule Model (MM) |Molecule Model]] entity). Some PDB entries (mostly NMR structures) contain multiple models, in such case, the sequential number ('''Index''') of the desired model to be displayed can be specified.
* '''Density Streaming''' - Creates a [[LiteMol:Hierarchy#Density Streaming (BDS) |Density Streaming]] for this molecule. Clicking on an atom or residue in the structure will instantly download and display the density data for the surrounding region. This solution is, in general, much faster than downloading the whole density map (often more than 1 GB). More details are available [http://webchem.ncbr.muni.cz/DensityServer here].
* '''PDBe Validation Report''' – Downloads wwPDB validation data for this molecule from PDBe and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''Ligand Validation Report''' - Downloads validation data for the ligands in this molecule from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB] and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''PDBe Sequence Annotations''' – Downloads sequence annotation data for this molecule from PDBe (collected from sources such as UniProt, InterProt, Pfam etc.) and creates a [[LiteMol:Hierarchy#Sequence Annotations (SA) | Sequence Annotations]] entity.

==Molecule Model (MM)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create an assembly (e.g. a virus capsid). Alternatively, just a part of the model can constitute a relevant assembly (e.g. the model contains a two molecules while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in the crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstrom) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for structures determined by NMR.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. This option is less automatic than '''Macromolecule Visual''' but more flexible. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding volume will be downloaded instantly. This can be useful when a part of the structure has already been downloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains to display the binding site).
* '''Update Model''' – Applicable when multiple models are included in the PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with the specified index (model number). Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model in addition to the current model.

 

==Group (G)==

This type of entity is used to organize multiple entities that are logically connected. For example, a group of selections containing different parts of a model (protein, ligand, and water) or a group of sequence annotations obtained from the same database.

==Molecule Model Selection (SM)==

This is an entity representing a subset of a molecule model. An example is one protein chain, one atom, or a set of all alanine residues. A selection can be created from either a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] entity or a [[LiteMol:Hierarchy#Molecule Visual (VM) | Molecule Visual]] entity. Selections are created using [[LiteMol:SelectionAlgebra | selection algebra language]].

Applicable actions:
* '''Visual''' – Create a visual representation of this selection. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Update Selection''' - Change the name of the [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] or change its definition using [[LiteMol:SelectionAlgebra | selection algebra language]]. (This action may not be not available for automatically generated selections.)

==Density Data (DD)==

Represents a three-dimensional map of electron density (for X-ray crystal structures) or electronic potential maps (for cryo-EM structures). Two types of maps are available for most crystal structures where structure factors are available in the PDB archive: '''2Fo-Fc''' and '''Fo-Fc'''.

Applicable actions:
* '''Surface''' – Creates a visualization of the density isosurface with the defined isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) |Density Visual]] entity).
* '''Interactive Surface''' – Creates a density isosurface which is shown only for a region of the molecule when you click on that region ([[LiteMol:Hierarchy#Interactive Surface (BIS) |Interactive Surface]] entity).
* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.

=Visualization=

This section contains entities that represent different visualizations of molecules and electron density maps.

==Molecule Visual (VM)==

[[File:LiteMol-cartoon.png | thumb | 250px | right| '''Cartoon''' visual for 1CBS. ]]

[[File:LiteMol-CA_trace.png | thumb | 250px | right| '''C-α trace''' visual for 1CBS. ]]

[[File:LiteMol-balls_and_sticks.png | thumb | 250px | right| '''Balls and Sticks''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-VDW_balls.png | thumb | 250px | right| '''VDW Balls''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-surface.png | thumb | 250px | right| '''Surface''' visual for 1CBS. ]]

A '''Molecule Visual''' is simply a visualization of a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] or its part. It is defined mostly by its type and coloring. These can be changed in '''Update Visual''' action. Click on the “+” icon next to “Type” or “Coloring” to modify other attributes. Some attributes are only available for certain types of visualization.

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Update Visual''' – Allows you to change the type of visualization and other attributes.

List of attributes:
* '''Type''' – One of the following:
** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, sheets, and unstructured regions.
** '''C-α Trace''' – Simplified wire-like representation of the backbone (no side-chains).
** '''Balls and Sticks''' – Atoms are represented by balls, bonds are shown as sticks connecting them. Keep in mind that most structures from X-ray and cryo-EM experiments do not provide positions of hydrogen atoms, so these are not visible in '''Ball and Sticks''' representation. There are some extra attributes that you can modify:
*** '''VDW''' – Indicates whether all atoms are shown as balls with uniform radius ('''VDW''' = Off) or ball's radius is based on the element's van der Waals radius ('''VDW''' = On).
*** '''Scale''' – (Only when '''VDW''' = On) The ratio between the ball's radius and the element's van der Waals radius.
*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the balls in Angstroms.
*** '''Bond Rds''' – The width (radius) of the sticks.
*** '''Bond''' – Color of the sticks.
** '''VDW Balls''' – Shows atoms as balls width radii corresponding to their van der Waals radii.
** '''Surface''' – Shows the smoothed boundary surface of the space “filled” by the molecule. There are some extra attributes that you can modify:
*** '''Probe Radius''' – How much space around an atom is considered as “filled” by this atom.
*** '''Smoothing''' – With lower values curvature of the surface around individual atoms will be more noticeable. With higher values the surface will be smoother.
*** '''Auto Detail''' - If set to On, the optimal level of detail is automatically derived from the size of the molecule. If set to Off, the level of detail can be adjusted manually (see the next item).
*** '''Detail''' – Defines how precisely the surface should be visualized. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource-demanding) when visualizing larger molecules.
*** '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).
* '''Detail''' – Defines how precisely the molecule should be visualized and can range from '''Very Low''' to '''Very High'''. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource-demanding) when visualizing larger molecules. If you choose '''Automatic''', LiteMol will infer the optimal level of detail from the molecule's size.
* '''Coloring''' – One of the following:
** '''Chain ID''' – Every chain will be shown in a different color.
** '''Entity ID''' – The same as '''Chain ID''' but identical chains are shown in the same color.
** '''Entity Type''' – Every type of entity (polymer, non-polymer, water) is shown in a different color.
** '''Residue Name''' – A different color is used for each type of residue.
** '''Element Symbol''' – A different color is used for each element.
** '''Rainbow (Chain)''' - Colors each chain in the colors of rainbow from N-terminus (red) to C-terminus (violet) (or from 5' to 3' in nucleic acids).
** '''Rainbow (Entity)''' - Similar to '''Rainbow (Chain)''', but identical chains are treated as a single longer chain (e.g. in a homodimer).
** '''Uniform Color''' – One selected color is used for the whole '''Visual'''.
* '''Highlight''' – The color in which this '''Visual''' will be temporarily colored when hovering over the '''Visual''' entity in the entity tree. When the cursor is placed on an atom or residue, it will be colored in the same way.
* '''Selection''' – If you create a [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] from this '''Visual''', it will be distinguished from the rest of the '''Visual''' by having this color.
* '''Opacity''' – The level of transparency of the '''Visual'''. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).

Please keep in mind that changing the type of a '''Visual''' will in fact remove the current visual and replace it with a new one, so all changes you have applied to the current '''Visual''' (such as creating a selection from it) will be lost! You can go to the superior entity and create a new '''Visual''' besides the current '''Visual'''.

 
==Density Visual (VDD)==

[[File:LiteMol-density_visual.png | thumb | 250px | right| Density isosurface at 1.5 σ (2Fo-Fc). ]]

Represents an isosurface of electron density, i.e. the surface in 3D connecting all the points with the value of electron density equal to a specified isovalue.

Applicable actions:
* '''Update Surface''' – Allows you to change the attributes of the visualization.

List of attributes:
* '''Iso value''' – The isovalue of electron density used for the visualized surface.
* '''Relative''' - Indicates whether normalized ('''Relative''' = On) or unnormalized ('''Relative''' = Off) density values are used. The relationship between the two values is as follows: ''Normalized'' = (''Unnormalized'' - ''Mean'') / ''Sigma''.
* '''Color''' – The color of the surface.
* '''Opacity''' – The level of transparency of the surface. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).
* '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).

 
==Interactive Surface (BIS)==

[[File:LiteMol-interactive_surface.png | thumb | 250px | right| Interactive density isosurface at 1.5 σ (2Fo-Fc) shown for a tryptophan residue and its surroundings with radius 2 Angstroms. ]]

This is a visualization of an isosurface of electron density, just as [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]]. The difference is that this surface is shown only when you click on a residue or an atom in the structure. The surface is shown only for the region around the selected residue or atom. An advantage of this interactive visualization is that the relevant region of density surface is not hindered by the rest of the molecule.

Three default '''Interactive Surfaces''' are created automatically when loading density data: blue surface corresponds to isovalue 1.5 in 2Fo-Fc density map. Green and red surfaces correspond to isovalues +3 and -3 in Fo-Fc density map.

Applicable actions:
* '''Update Interactive Surface''' – Change the attributes of the visualization. These attributes are the same as in the case of [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity. An extra attribute is '''Radius''', which allows you to change the size of the region for which the isosurface is shown. Attribute '''Show''' toggles between interactive visualization around the selected region ('''Show''' = Around Selection) and static visualization of the whole map ('''Show''' = Everything, practically equivalent to [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity).

 
=Annotations=

This section describes entities which can store additional information about the structures, such as validation issues or sequence annotations.

==Validation Report (VR)==

[[File:LiteMol-validation_report.png | thumb | 250px | right| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]

[[File:LiteMol-ligand_validation_report.png | thumb | 250px | right| An oligosaccharide in the structure of ribosom-inactivating protein abrin-a (1ABR) colored by the '''Ligand Validation Report'''. The right-most residue is missing an atom. One of the residues in the center has an atom with wrongly annotated chirality. ]]

Represents validation data for this molecule from PDBe. The full validation report in PDF can be downloaded from the [http://www.ebi.ac.uk/pdbe/ PDBe site] (find your molecule, click ''Details'' in ''Experiments and Validation'' section, and then ''Full Validation Report'' in the right panel). An example of a validation report is available [http://www.ebi.ac.uk/pdbe/entry-files/download/1rtc_full_validation.pdf here].

Another type of '''Validation Report''' entity is '''Ligand Validation Report''', which represents validation data for the ligands in this molecule. This data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB].

Applicable actions:
* '''Apply Coloring''' – The structure will be colored according the validation data. For '''PDBe Validation Report''' the color of each residue depends on the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2, and red = 3 or more. For '''Ligand Validation Report''' the residues with missing atoms are colored in red. Also the atoms with wrong chirality are shown in red (examples can be found in PDB entry 1ABR). The correct residues are shown in green.

 
==Sequence Annotations (SA)==

[[File:LiteMol-annotation.png | thumb | 250px | right| Structure of ricin A chain (4Q2V). The orange color indicates the part annotated as ''Ribosome-inactivating protein, subdomain 1'' by InterPro database. ]]

Represents a collection of sequence annotations from PDBe, grouped by the source database.

==Sequence Annotation (SA)==

Represents a single sequence annotation, i.e. assignment of a name to a part of the structure. When you hover above this entity or click on it, the corresponding part of the structure will be shown in a distinctive color.

Applicable actions:
* '''Update PDBe Sequence Annotation''' – Allows you to change the color used for this part of the structure.

 
=Raw Data=

This section contains entities that store data from a file, no matter what these data represent and how their are encoded (i.e. original data from a file before they are parsed). The user will encounter them mostly when loading files from a disk or a URL.

==String Data (SD)==
This entity represents data loaded from a file in textual format (e.g. mmCIF file or PDB file).

Applicable actions:
* '''Molecule''' – Treats the data as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. Make sure to select the appropriate format.
* '''Density Data''' – Treats the data as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity.
* '''CIF Dictionary''' – Treats the data as a CIF dictionary and creates a [[LiteMol:Hierarchy#CIF Dictionary (CD) | CIF Dictionary]] entity. CIF dictionary itself can contain various kinds of data, including molecular structures or density maps.

==Binary Data (BD)==
This entity represents data loaded from a binary file (not human-readable, e.g. [https://github.com/dsehnal/BinaryCIF BinaryCIF] file or CCP4 density file). '''Binary Data''' provides exactly the same actions as [[LiteMol:Hierarchy#String Data (SD) | String Data]].

==CIF Dictionary (CD)==
This entity represents data encoded in a CIF dictionary, which is a flexible format for various kinds of data, so it can contain molecular structures or density maps. A single CIF dictionary can even contain multiple objects (e.g. two density maps: 2Fo-Fc and Fo-Fc).

Applicable actions:
* '''Molecule''' – Treats the data in the '''CIF dictionary''' as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').
* '''Density Data''' – Treats the data in the '''CIF dictionary''' as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').

LiteMol:Hierarchy

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Matthew: /* Molecule Model Selection (SM) */ mjc edit

[[File:LiteMol-hierarchy.png | thumb | 200px | right| An example of an '''entity tree'''. ]]

All data in LiteMol are organized in a hierarchy represented by the '''entity tree'''. This tree is shown in LiteMol's left panel. When you click on an entity in the tree, you will see all actions applicable to this entity listed in the right panel.

This page lists all types of entities and explains the actions they provide. The entity types can be divided into four sections: Structures, Visualization, Annotations, and Raw Data.

=Structures=

This section describes the entities used for representation of molecular models and electron density maps. It does not contain any information about how these data are visualized.

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set:
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file.
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action.
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.

==Molecule (M)==

A '''Molecule''' entity represents a set of structural data for a '''Molecule''' (which corresponds to one PDB entry or one mmCIF file).

Applicable actions:
* '''Model''' – Creates a model of the molecule ([[LiteMol:Hierarchy#Molecule Model (MM) |Molecule Model]] entity). Some PDB entries (mostly NMR structures) contain multiple models, in such case, the sequential number ('''Index''') of the desired model to be displayed can be specified.
* '''Density Streaming''' - Creates a [[LiteMol:Hierarchy#Density Streaming (BDS) |Density Streaming]] for this molecule. Clicking on an atom or residue in the structure will instantly download and display the density data for the surrounding region. This solution is, in general, much faster than downloading the whole density map (often more than 1 GB). More details are available [http://webchem.ncbr.muni.cz/DensityServer here].
* '''PDBe Validation Report''' – Downloads wwPDB validation data for this molecule from PDBe and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''Ligand Validation Report''' - Downloads validation data for the ligands in this molecule from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB] and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''PDBe Sequence Annotations''' – Downloads sequence annotation data for this molecule from PDBe (collected from sources such as UniProt, InterProt, Pfam etc.) and creates a [[LiteMol:Hierarchy#Sequence Annotations (SA) | Sequence Annotations]] entity.

==Molecule Model (MM)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create an assembly (e.g. a virus capsid). Alternatively, just a part of the model can constitute a relevant assembly (e.g. the model contains a two molecules while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in the crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstrom) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for structures determined by NMR.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. This option is less automatic than '''Macromolecule Visual''' but more flexible. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding volume will be downloaded instantly. This can be useful when a part of the structure has already been downloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains to display the binding site).
* '''Update Model''' – Applicable when multiple models are included in the PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with the specified index (model number). Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model in addition to the current model.

 

==Group (G)==

This type of entity is used to organize multiple entities that are logically connected. For example, a group of selections containing different parts of a model (protein, ligand, and water) or a group of sequence annotations obtained from the same database.

==Molecule Model Selection (SM)==

This is an entity representing a subset of a molecule model. An example is one protein chain, one atom, or a set of all alanine residues. A selection can be created from either a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] entity or a [[LiteMol:Hierarchy#Molecule Visual (VM) | Molecule Visual]] entity. Selections are created using [[LiteMol:SelectionAlgebra | selection algebra language]].

Applicable actions:
* '''Visual''' – Create a visual representation of this selection. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Update Selection''' - Change the name of the [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] or change its definition using [[LiteMol:SelectionAlgebra | selection algebra language]]. (This action may not be not available for automatically generated selections.)

==Density Data (DD)==

Represents a three-dimensional map of electron density. Two types of maps are available for most crystal structures: '''2Fo-Fc''' and '''Fo-Fc'''. Only one map is available for cryo-EM structures.

Applicable actions:
* '''Surface''' – Creates a visualization of the density isosurface with given isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) |Density Visual]] entity).
* '''Interactive Surface''' – Creates a density isosurface which is shown only for a region of the molecule when you click on that region ([[LiteMol:Hierarchy#Interactive Surface (BIS) |Interactive Surface]] entity).
* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.

=Visualization=

This section contains entities that represent different visualizations of molecules and electron density maps.

==Molecule Visual (VM)==

[[File:LiteMol-cartoon.png | thumb | 250px | right| '''Cartoon''' visual for 1CBS. ]]

[[File:LiteMol-CA_trace.png | thumb | 250px | right| '''C-α trace''' visual for 1CBS. ]]

[[File:LiteMol-balls_and_sticks.png | thumb | 250px | right| '''Balls and Sticks''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-VDW_balls.png | thumb | 250px | right| '''VDW Balls''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-surface.png | thumb | 250px | right| '''Surface''' visual for 1CBS. ]]

A '''Molecule Visual''' is simply a visualization of a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] or its part. It is defined mostly by its type and coloring. These can be changed in '''Update Visual''' action. Click on the “+” icon next to “Type” or “Coloring” to modify other attributes. Some attributes are only available for certain types of visualization.

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Update Visual''' – Allows you to change the type of visualization and other attributes.

List of attributes:
* '''Type''' – One of the following:
** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, sheets, and unstructured regions.
** '''C-α Trace''' – Simplified wire-like representation of the backbone (no side-chains).
** '''Balls and Sticks''' – Atoms are represented by balls, bonds are shown as sticks connecting them. Keep in mind that most structures from X-ray and cryo-EM experiments do not provide positions of hydrogen atoms, so these are not visible in '''Ball and Sticks''' representation. There are some extra attributes that you can modify:
*** '''VDW''' – Indicates whether all atoms are shown as balls with uniform radius ('''VDW''' = Off) or ball's radius is based on the element's van der Waals radius ('''VDW''' = On).
*** '''Scale''' – (Only when '''VDW''' = On) The ratio between the ball's radius and the element's van der Waals radius.
*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the balls in Angstroms.
*** '''Bond Rds''' – The width (radius) of the sticks.
*** '''Bond''' – Color of the sticks.
** '''VDW Balls''' – Shows atoms as balls width radii corresponding to their van der Waals radii.
** '''Surface''' – Shows the smoothed boundary surface of the space “filled” by the molecule. There are some extra attributes that you can modify:
*** '''Probe Radius''' – How much space around an atom is considered as “filled” by this atom.
*** '''Smoothing''' – With lower values curvature of the surface around individual atoms will be more noticeable. With higher values the surface will be smoother.
*** '''Auto Detail''' - If set to On, the optimal level of detail is automatically derived from the size of the molecule. If set to Off, the level of detail can be adjusted manually (see the next item).
*** '''Detail''' – Defines how precisely the surface should be visualized. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource-demanding) when visualizing larger molecules.
*** '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).
* '''Detail''' – Defines how precisely the molecule should be visualized and can range from '''Very Low''' to '''Very High'''. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource-demanding) when visualizing larger molecules. If you choose '''Automatic''', LiteMol will infer the optimal level of detail from the molecule's size.
* '''Coloring''' – One of the following:
** '''Chain ID''' – Every chain will be shown in a different color.
** '''Entity ID''' – The same as '''Chain ID''' but identical chains are shown in the same color.
** '''Entity Type''' – Every type of entity (polymer, non-polymer, water) is shown in a different color.
** '''Residue Name''' – A different color is used for each type of residue.
** '''Element Symbol''' – A different color is used for each element.
** '''Rainbow (Chain)''' - Colors each chain in the colors of rainbow from N-terminus (red) to C-terminus (violet) (or from 5' to 3' in nucleic acids).
** '''Rainbow (Entity)''' - Similar to '''Rainbow (Chain)''', but identical chains are treated as a single longer chain (e.g. in a homodimer).
** '''Uniform Color''' – One selected color is used for the whole '''Visual'''.
* '''Highlight''' – The color in which this '''Visual''' will be temporarily colored when hovering over the '''Visual''' entity in the entity tree. When the cursor is placed on an atom or residue, it will be colored in the same way.
* '''Selection''' – If you create a [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] from this '''Visual''', it will be distinguished from the rest of the '''Visual''' by having this color.
* '''Opacity''' – The level of transparency of the '''Visual'''. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).

Please keep in mind that changing the type of a '''Visual''' will in fact remove the current visual and replace it with a new one, so all changes you have applied to the current '''Visual''' (such as creating a selection from it) will be lost! You can go to the superior entity and create a new '''Visual''' besides the current '''Visual'''.

 
==Density Visual (VDD)==

[[File:LiteMol-density_visual.png | thumb | 250px | right| Density isosurface at 1.5 σ (2Fo-Fc). ]]

Represents an isosurface of electron density, i.e. the surface in 3D connecting all the points with the value of electron density equal to a specified isovalue.

Applicable actions:
* '''Update Surface''' – Allows you to change the attributes of the visualization.

List of attributes:
* '''Iso value''' – The isovalue of electron density used for the visualized surface.
* '''Relative''' - Indicates whether normalized ('''Relative''' = On) or unnormalized ('''Relative''' = Off) density values are used. The relationship between the two values is as follows: ''Normalized'' = (''Unnormalized'' - ''Mean'') / ''Sigma''.
* '''Color''' – The color of the surface.
* '''Opacity''' – The level of transparency of the surface. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).
* '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).

 
==Interactive Surface (BIS)==

[[File:LiteMol-interactive_surface.png | thumb | 250px | right| Interactive density isosurface at 1.5 σ (2Fo-Fc) shown for a tryptophan residue and its surroundings with radius 2 Angstroms. ]]

This is a visualization of an isosurface of electron density, just as [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]]. The difference is that this surface is shown only when you click on a residue or an atom in the structure. The surface is shown only for the region around the selected residue or atom. An advantage of this interactive visualization is that the relevant region of density surface is not hindered by the rest of the molecule.

Three default '''Interactive Surfaces''' are created automatically when loading density data: blue surface corresponds to isovalue 1.5 in 2Fo-Fc density map. Green and red surfaces correspond to isovalues +3 and -3 in Fo-Fc density map.

Applicable actions:
* '''Update Interactive Surface''' – Change the attributes of the visualization. These attributes are the same as in the case of [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity. An extra attribute is '''Radius''', which allows you to change the size of the region for which the isosurface is shown. Attribute '''Show''' toggles between interactive visualization around the selected region ('''Show''' = Around Selection) and static visualization of the whole map ('''Show''' = Everything, practically equivalent to [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity).

 
=Annotations=

This section describes entities which can store additional information about the structures, such as validation issues or sequence annotations.

==Validation Report (VR)==

[[File:LiteMol-validation_report.png | thumb | 250px | right| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]

[[File:LiteMol-ligand_validation_report.png | thumb | 250px | right| An oligosaccharide in the structure of ribosom-inactivating protein abrin-a (1ABR) colored by the '''Ligand Validation Report'''. The right-most residue is missing an atom. One of the residues in the center has an atom with wrongly annotated chirality. ]]

Represents validation data for this molecule from PDBe. The full validation report in PDF can be downloaded from the [http://www.ebi.ac.uk/pdbe/ PDBe site] (find your molecule, click ''Details'' in ''Experiments and Validation'' section, and then ''Full Validation Report'' in the right panel). An example of a validation report is available [http://www.ebi.ac.uk/pdbe/entry-files/download/1rtc_full_validation.pdf here].

Another type of '''Validation Report''' entity is '''Ligand Validation Report''', which represents validation data for the ligands in this molecule. This data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB].

Applicable actions:
* '''Apply Coloring''' – The structure will be colored according the validation data. For '''PDBe Validation Report''' the color of each residue depends on the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2, and red = 3 or more. For '''Ligand Validation Report''' the residues with missing atoms are colored in red. Also the atoms with wrong chirality are shown in red (examples can be found in PDB entry 1ABR). The correct residues are shown in green.

 
==Sequence Annotations (SA)==

[[File:LiteMol-annotation.png | thumb | 250px | right| Structure of ricin A chain (4Q2V). The orange color indicates the part annotated as ''Ribosome-inactivating protein, subdomain 1'' by InterPro database. ]]

Represents a collection of sequence annotations from PDBe, grouped by the source database.

==Sequence Annotation (SA)==

Represents a single sequence annotation, i.e. assignment of a name to a part of the structure. When you hover above this entity or click on it, the corresponding part of the structure will be shown in a distinctive color.

Applicable actions:
* '''Update PDBe Sequence Annotation''' – Allows you to change the color used for this part of the structure.

 
=Raw Data=

This section contains entities that store data from a file, no matter what these data represent and how their are encoded (i.e. original data from a file before they are parsed). The user will encounter them mostly when loading files from a disk or a URL.

==String Data (SD)==
This entity represents data loaded from a file in textual format (e.g. mmCIF file or PDB file).

Applicable actions:
* '''Molecule''' – Treats the data as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. Make sure to select the appropriate format.
* '''Density Data''' – Treats the data as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity.
* '''CIF Dictionary''' – Treats the data as a CIF dictionary and creates a [[LiteMol:Hierarchy#CIF Dictionary (CD) | CIF Dictionary]] entity. CIF dictionary itself can contain various kinds of data, including molecular structures or density maps.

==Binary Data (BD)==
This entity represents data loaded from a binary file (not human-readable, e.g. [https://github.com/dsehnal/BinaryCIF BinaryCIF] file or CCP4 density file). '''Binary Data''' provides exactly the same actions as [[LiteMol:Hierarchy#String Data (SD) | String Data]].

==CIF Dictionary (CD)==
This entity represents data encoded in a CIF dictionary, which is a flexible format for various kinds of data, so it can contain molecular structures or density maps. A single CIF dictionary can even contain multiple objects (e.g. two density maps: 2Fo-Fc and Fo-Fc).

Applicable actions:
* '''Molecule''' – Treats the data in the '''CIF dictionary''' as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').
* '''Density Data''' – Treats the data in the '''CIF dictionary''' as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').

LiteMol:Hierarchy

2017-05-05T09:54:03Z

Matthew: /* Group (G) */ mjc edit

[[File:LiteMol-hierarchy.png | thumb | 200px | right| An example of an '''entity tree'''. ]]

All data in LiteMol are organized in a hierarchy represented by the '''entity tree'''. This tree is shown in LiteMol's left panel. When you click on an entity in the tree, you will see all actions applicable to this entity listed in the right panel.

This page lists all types of entities and explains the actions they provide. The entity types can be divided into four sections: Structures, Visualization, Annotations, and Raw Data.

=Structures=

This section describes the entities used for representation of molecular models and electron density maps. It does not contain any information about how these data are visualized.

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set:
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file.
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action.
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.

==Molecule (M)==

A '''Molecule''' entity represents a set of structural data for a '''Molecule''' (which corresponds to one PDB entry or one mmCIF file).

Applicable actions:
* '''Model''' – Creates a model of the molecule ([[LiteMol:Hierarchy#Molecule Model (MM) |Molecule Model]] entity). Some PDB entries (mostly NMR structures) contain multiple models, in such case, the sequential number ('''Index''') of the desired model to be displayed can be specified.
* '''Density Streaming''' - Creates a [[LiteMol:Hierarchy#Density Streaming (BDS) |Density Streaming]] for this molecule. Clicking on an atom or residue in the structure will instantly download and display the density data for the surrounding region. This solution is, in general, much faster than downloading the whole density map (often more than 1 GB). More details are available [http://webchem.ncbr.muni.cz/DensityServer here].
* '''PDBe Validation Report''' – Downloads wwPDB validation data for this molecule from PDBe and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''Ligand Validation Report''' - Downloads validation data for the ligands in this molecule from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB] and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''PDBe Sequence Annotations''' – Downloads sequence annotation data for this molecule from PDBe (collected from sources such as UniProt, InterProt, Pfam etc.) and creates a [[LiteMol:Hierarchy#Sequence Annotations (SA) | Sequence Annotations]] entity.

==Molecule Model (MM)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create an assembly (e.g. a virus capsid). Alternatively, just a part of the model can constitute a relevant assembly (e.g. the model contains a two molecules while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in the crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstrom) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for structures determined by NMR.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. This option is less automatic than '''Macromolecule Visual''' but more flexible. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding volume will be downloaded instantly. This can be useful when a part of the structure has already been downloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains to display the binding site).
* '''Update Model''' – Applicable when multiple models are included in the PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with the specified index (model number). Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model in addition to the current model.

 

==Group (G)==

This type of entity is used to organize multiple entities that are logically connected. For example, a group of selections containing different parts of a model (protein, ligand, and water) or a group of sequence annotations obtained from the same database.

==Molecule Model Selection (SM)==

This is an entity representing a subset of a molecule model. An example is one protein chain, one atom, or a set of all alanine residues. A selection can be created from either a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] entity or a [[LiteMol:Hierarchy#Molecule Visual (VM) | Molecule Visual]] entity. Selections are created using [[LiteMol:SelectionAlgebra | selection algebra language]].

Applicable actions:
* '''Visual''' – Create a visual representation of this selection. Type, coloring, and other attributes of created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Update Selection''' - Change the name of the [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] or change its definition using [[LiteMol:SelectionAlgebra | selection algebra language]]. (This action may not be not available for automatically generated selections.)

==Density Data (DD)==

Represents a three-dimensional map of electron density. Two types of maps are available for most crystal structures: '''2Fo-Fc''' and '''Fo-Fc'''. Only one map is available for cryo-EM structures.

Applicable actions:
* '''Surface''' – Creates a visualization of the density isosurface with given isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) |Density Visual]] entity).
* '''Interactive Surface''' – Creates a density isosurface which is shown only for a region of the molecule when you click on that region ([[LiteMol:Hierarchy#Interactive Surface (BIS) |Interactive Surface]] entity).
* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.

=Visualization=

This section contains entities that represent different visualizations of molecules and electron density maps.

==Molecule Visual (VM)==

[[File:LiteMol-cartoon.png | thumb | 250px | right| '''Cartoon''' visual for 1CBS. ]]

[[File:LiteMol-CA_trace.png | thumb | 250px | right| '''C-α trace''' visual for 1CBS. ]]

[[File:LiteMol-balls_and_sticks.png | thumb | 250px | right| '''Balls and Sticks''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-VDW_balls.png | thumb | 250px | right| '''VDW Balls''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-surface.png | thumb | 250px | right| '''Surface''' visual for 1CBS. ]]

A '''Molecule Visual''' is simply a visualization of a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] or its part. It is defined mostly by its type and coloring. These can be changed in '''Update Visual''' action. Click on the “+” icon next to “Type” or “Coloring” to modify other attributes. Some attributes are only available for certain types of visualization.

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Update Visual''' – Allows you to change the type of visualization and other attributes.

List of attributes:
* '''Type''' – One of the following:
** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, sheets, and unstructured regions.
** '''C-α Trace''' – Simplified wire-like representation of the backbone (no side-chains).
** '''Balls and Sticks''' – Atoms are represented by balls, bonds are shown as sticks connecting them. Keep in mind that most structures from X-ray and cryo-EM experiments do not provide positions of hydrogen atoms, so these are not visible in '''Ball and Sticks''' representation. There are some extra attributes that you can modify:
*** '''VDW''' – Indicates whether all atoms are shown as balls with uniform radius ('''VDW''' = Off) or ball's radius is based on the element's van der Waals radius ('''VDW''' = On).
*** '''Scale''' – (Only when '''VDW''' = On) The ratio between the ball's radius and the element's van der Waals radius.
*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the balls in Angstroms.
*** '''Bond Rds''' – The width (radius) of the sticks.
*** '''Bond''' – Color of the sticks.
** '''VDW Balls''' – Shows atoms as balls width radii corresponding to their van der Waals radii.
** '''Surface''' – Shows the smoothed boundary surface of the space “filled” by the molecule. There are some extra attributes that you can modify:
*** '''Probe Radius''' – How much space around an atom is considered as “filled” by this atom.
*** '''Smoothing''' – With lower values curvature of the surface around individual atoms will be more noticeable. With higher values the surface will be smoother.
*** '''Auto Detail''' - If set to On, the optimal level of detail is automatically derived from the size of the molecule. If set to Off, the level of detail can be adjusted manually (see the next item).
*** '''Detail''' – Defines how precisely the surface should be visualized. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource-demanding) when visualizing larger molecules.
*** '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).
* '''Detail''' – Defines how precisely the molecule should be visualized and can range from '''Very Low''' to '''Very High'''. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource-demanding) when visualizing larger molecules. If you choose '''Automatic''', LiteMol will infer the optimal level of detail from the molecule's size.
* '''Coloring''' – One of the following:
** '''Chain ID''' – Every chain will be shown in a different color.
** '''Entity ID''' – The same as '''Chain ID''' but identical chains are shown in the same color.
** '''Entity Type''' – Every type of entity (polymer, non-polymer, water) is shown in a different color.
** '''Residue Name''' – A different color is used for each type of residue.
** '''Element Symbol''' – A different color is used for each element.
** '''Rainbow (Chain)''' - Colors each chain in the colors of rainbow from N-terminus (red) to C-terminus (violet) (or from 5' to 3' in nucleic acids).
** '''Rainbow (Entity)''' - Similar to '''Rainbow (Chain)''', but identical chains are treated as a single longer chain (e.g. in a homodimer).
** '''Uniform Color''' – One selected color is used for the whole '''Visual'''.
* '''Highlight''' – The color in which this '''Visual''' will be temporarily colored when hovering over the '''Visual''' entity in the entity tree. When the cursor is placed on an atom or residue, it will be colored in the same way.
* '''Selection''' – If you create a [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] from this '''Visual''', it will be distinguished from the rest of the '''Visual''' by having this color.
* '''Opacity''' – The level of transparency of the '''Visual'''. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).

Please keep in mind that changing the type of a '''Visual''' will in fact remove the current visual and replace it with a new one, so all changes you have applied to the current '''Visual''' (such as creating a selection from it) will be lost! You can go to the superior entity and create a new '''Visual''' besides the current '''Visual'''.

 
==Density Visual (VDD)==

[[File:LiteMol-density_visual.png | thumb | 250px | right| Density isosurface at 1.5 σ (2Fo-Fc). ]]

Represents an isosurface of electron density, i.e. the surface in 3D connecting all the points with the value of electron density equal to a specified isovalue.

Applicable actions:
* '''Update Surface''' – Allows you to change the attributes of the visualization.

List of attributes:
* '''Iso value''' – The isovalue of electron density used for the visualized surface.
* '''Relative''' - Indicates whether normalized ('''Relative''' = On) or unnormalized ('''Relative''' = Off) density values are used. The relationship between the two values is as follows: ''Normalized'' = (''Unnormalized'' - ''Mean'') / ''Sigma''.
* '''Color''' – The color of the surface.
* '''Opacity''' – The level of transparency of the surface. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).
* '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).

 
==Interactive Surface (BIS)==

[[File:LiteMol-interactive_surface.png | thumb | 250px | right| Interactive density isosurface at 1.5 σ (2Fo-Fc) shown for a tryptophan residue and its surroundings with radius 2 Angstroms. ]]

This is a visualization of an isosurface of electron density, just as [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]]. The difference is that this surface is shown only when you click on a residue or an atom in the structure. The surface is shown only for the region around the selected residue or atom. An advantage of this interactive visualization is that the relevant region of density surface is not hindered by the rest of the molecule.

Three default '''Interactive Surfaces''' are created automatically when loading density data: blue surface corresponds to isovalue 1.5 in 2Fo-Fc density map. Green and red surfaces correspond to isovalues +3 and -3 in Fo-Fc density map.

Applicable actions:
* '''Update Interactive Surface''' – Change the attributes of the visualization. These attributes are the same as in the case of [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity. An extra attribute is '''Radius''', which allows you to change the size of the region for which the isosurface is shown. Attribute '''Show''' toggles between interactive visualization around the selected region ('''Show''' = Around Selection) and static visualization of the whole map ('''Show''' = Everything, practically equivalent to [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity).

 
=Annotations=

This section describes entities which can store additional information about the structures, such as validation issues or sequence annotations.

==Validation Report (VR)==

[[File:LiteMol-validation_report.png | thumb | 250px | right| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]

[[File:LiteMol-ligand_validation_report.png | thumb | 250px | right| An oligosaccharide in the structure of ribosom-inactivating protein abrin-a (1ABR) colored by the '''Ligand Validation Report'''. The right-most residue is missing an atom. One of the residues in the center has an atom with wrongly annotated chirality. ]]

Represents validation data for this molecule from PDBe. The full validation report in PDF can be downloaded from the [http://www.ebi.ac.uk/pdbe/ PDBe site] (find your molecule, click ''Details'' in ''Experiments and Validation'' section, and then ''Full Validation Report'' in the right panel). An example of a validation report is available [http://www.ebi.ac.uk/pdbe/entry-files/download/1rtc_full_validation.pdf here].

Another type of '''Validation Report''' entity is '''Ligand Validation Report''', which represents validation data for the ligands in this molecule. This data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB].

Applicable actions:
* '''Apply Coloring''' – The structure will be colored according the validation data. For '''PDBe Validation Report''' the color of each residue depends on the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2, and red = 3 or more. For '''Ligand Validation Report''' the residues with missing atoms are colored in red. Also the atoms with wrong chirality are shown in red (examples can be found in PDB entry 1ABR). The correct residues are shown in green.

 
==Sequence Annotations (SA)==

[[File:LiteMol-annotation.png | thumb | 250px | right| Structure of ricin A chain (4Q2V). The orange color indicates the part annotated as ''Ribosome-inactivating protein, subdomain 1'' by InterPro database. ]]

Represents a collection of sequence annotations from PDBe, grouped by the source database.

==Sequence Annotation (SA)==

Represents a single sequence annotation, i.e. assignment of a name to a part of the structure. When you hover above this entity or click on it, the corresponding part of the structure will be shown in a distinctive color.

Applicable actions:
* '''Update PDBe Sequence Annotation''' – Allows you to change the color used for this part of the structure.

 
=Raw Data=

This section contains entities that store data from a file, no matter what these data represent and how their are encoded (i.e. original data from a file before they are parsed). The user will encounter them mostly when loading files from a disk or a URL.

==String Data (SD)==
This entity represents data loaded from a file in textual format (e.g. mmCIF file or PDB file).

Applicable actions:
* '''Molecule''' – Treats the data as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. Make sure to select the appropriate format.
* '''Density Data''' – Treats the data as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity.
* '''CIF Dictionary''' – Treats the data as a CIF dictionary and creates a [[LiteMol:Hierarchy#CIF Dictionary (CD) | CIF Dictionary]] entity. CIF dictionary itself can contain various kinds of data, including molecular structures or density maps.

==Binary Data (BD)==
This entity represents data loaded from a binary file (not human-readable, e.g. [https://github.com/dsehnal/BinaryCIF BinaryCIF] file or CCP4 density file). '''Binary Data''' provides exactly the same actions as [[LiteMol:Hierarchy#String Data (SD) | String Data]].

==CIF Dictionary (CD)==
This entity represents data encoded in a CIF dictionary, which is a flexible format for various kinds of data, so it can contain molecular structures or density maps. A single CIF dictionary can even contain multiple objects (e.g. two density maps: 2Fo-Fc and Fo-Fc).

Applicable actions:
* '''Molecule''' – Treats the data in the '''CIF dictionary''' as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').
* '''Density Data''' – Treats the data in the '''CIF dictionary''' as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').

LiteMol:Hierarchy

2017-05-05T09:49:14Z

Matthew: /* Molecule Model (MM) */ mjc edit

[[File:LiteMol-hierarchy.png | thumb | 200px | right| An example of an '''entity tree'''. ]]

All data in LiteMol are organized in a hierarchy represented by the '''entity tree'''. This tree is shown in LiteMol's left panel. When you click on an entity in the tree, you will see all actions applicable to this entity listed in the right panel.

This page lists all types of entities and explains the actions they provide. The entity types can be divided into four sections: Structures, Visualization, Annotations, and Raw Data.

=Structures=

This section describes the entities used for representation of molecular models and electron density maps. It does not contain any information about how these data are visualized.

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set:
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file.
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action.
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.

==Molecule (M)==

A '''Molecule''' entity represents a set of structural data for a '''Molecule''' (which corresponds to one PDB entry or one mmCIF file).

Applicable actions:
* '''Model''' – Creates a model of the molecule ([[LiteMol:Hierarchy#Molecule Model (MM) |Molecule Model]] entity). Some PDB entries (mostly NMR structures) contain multiple models, in such case, the sequential number ('''Index''') of the desired model to be displayed can be specified.
* '''Density Streaming''' - Creates a [[LiteMol:Hierarchy#Density Streaming (BDS) |Density Streaming]] for this molecule. Clicking on an atom or residue in the structure will instantly download and display the density data for the surrounding region. This solution is, in general, much faster than downloading the whole density map (often more than 1 GB). More details are available [http://webchem.ncbr.muni.cz/DensityServer here].
* '''PDBe Validation Report''' – Downloads wwPDB validation data for this molecule from PDBe and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''Ligand Validation Report''' - Downloads validation data for the ligands in this molecule from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB] and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''PDBe Sequence Annotations''' – Downloads sequence annotation data for this molecule from PDBe (collected from sources such as UniProt, InterProt, Pfam etc.) and creates a [[LiteMol:Hierarchy#Sequence Annotations (SA) | Sequence Annotations]] entity.

==Molecule Model (MM)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create an assembly (e.g. a virus capsid). Alternatively, just a part of the model can constitute a relevant assembly (e.g. the model contains a two molecules while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in the crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstrom) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for structures determined by NMR.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. This option is less automatic than '''Macromolecule Visual''' but more flexible. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding volume will be downloaded instantly. This can be useful when a part of the structure has already been downloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains to display the binding site).
* '''Update Model''' – Applicable when multiple models are included in the PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with the specified index (model number). Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model in addition to the current model.

 

==Group (G)==

This type of entity is merely used to organize multiple entities that are logically connected. An example is a group of selections containing different parts of a model (protein, ligand, and water) or a group of sequence annotations obtained from the same database.

==Molecule Model Selection (SM)==

This is an entity representing a subset of a molecule model. An example is one protein chain, one atom, or a set of all alanine residues. A selection can be created from either a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] entity or a [[LiteMol:Hierarchy#Molecule Visual (VM) | Molecule Visual]] entity. Selections are created using [[LiteMol:SelectionAlgebra | selection algebra language]].

Applicable actions:
* '''Visual''' – Create a visual representation of this selection. Type, coloring, and other attributes of created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Update Selection''' - Change the name of the [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] or change its definition using [[LiteMol:SelectionAlgebra | selection algebra language]]. (This action may not be not available for automatically generated selections.)

==Density Data (DD)==

Represents a three-dimensional map of electron density. Two types of maps are available for most crystal structures: '''2Fo-Fc''' and '''Fo-Fc'''. Only one map is available for cryo-EM structures.

Applicable actions:
* '''Surface''' – Creates a visualization of the density isosurface with given isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) |Density Visual]] entity).
* '''Interactive Surface''' – Creates a density isosurface which is shown only for a region of the molecule when you click on that region ([[LiteMol:Hierarchy#Interactive Surface (BIS) |Interactive Surface]] entity).
* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.

=Visualization=

This section contains entities that represent different visualizations of molecules and electron density maps.

==Molecule Visual (VM)==

[[File:LiteMol-cartoon.png | thumb | 250px | right| '''Cartoon''' visual for 1CBS. ]]

[[File:LiteMol-CA_trace.png | thumb | 250px | right| '''C-α trace''' visual for 1CBS. ]]

[[File:LiteMol-balls_and_sticks.png | thumb | 250px | right| '''Balls and Sticks''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-VDW_balls.png | thumb | 250px | right| '''VDW Balls''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-surface.png | thumb | 250px | right| '''Surface''' visual for 1CBS. ]]

A '''Molecule Visual''' is simply a visualization of a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] or its part. It is defined mostly by its type and coloring. These can be changed in '''Update Visual''' action. Click on the “+” icon next to “Type” or “Coloring” to modify other attributes. Some attributes are only available for certain types of visualization.

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Update Visual''' – Allows you to change the type of visualization and other attributes.

List of attributes:
* '''Type''' – One of the following:
** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, sheets, and unstructured regions.
** '''C-α Trace''' – Simplified wire-like representation of the backbone (no side-chains).
** '''Balls and Sticks''' – Atoms are represented by balls, bonds are shown as sticks connecting them. Keep in mind that most structures from X-ray and cryo-EM experiments do not provide positions of hydrogen atoms, so these are not visible in '''Ball and Sticks''' representation. There are some extra attributes that you can modify:
*** '''VDW''' – Indicates whether all atoms are shown as balls with uniform radius ('''VDW''' = Off) or ball's radius is based on the element's van der Waals radius ('''VDW''' = On).
*** '''Scale''' – (Only when '''VDW''' = On) The ratio between the ball's radius and the element's van der Waals radius.
*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the balls in Angstroms.
*** '''Bond Rds''' – The width (radius) of the sticks.
*** '''Bond''' – Color of the sticks.
** '''VDW Balls''' – Shows atoms as balls width radii corresponding to their van der Waals radii.
** '''Surface''' – Shows the smoothed boundary surface of the space “filled” by the molecule. There are some extra attributes that you can modify:
*** '''Probe Radius''' – How much space around an atom is considered as “filled” by this atom.
*** '''Smoothing''' – With lower values curvature of the surface around individual atoms will be more noticeable. With higher values the surface will be smoother.
*** '''Auto Detail''' - If set to On, the optimal level of detail is automatically derived from the size of the molecule. If set to Off, the level of detail can be adjusted manually (see the next item).
*** '''Detail''' – Defines how precisely the surface should be visualized. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource-demanding) when visualizing larger molecules.
*** '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).
* '''Detail''' – Defines how precisely the molecule should be visualized and can range from '''Very Low''' to '''Very High'''. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource-demanding) when visualizing larger molecules. If you choose '''Automatic''', LiteMol will infer the optimal level of detail from the molecule's size.
* '''Coloring''' – One of the following:
** '''Chain ID''' – Every chain will be shown in a different color.
** '''Entity ID''' – The same as '''Chain ID''' but identical chains are shown in the same color.
** '''Entity Type''' – Every type of entity (polymer, non-polymer, water) is shown in a different color.
** '''Residue Name''' – A different color is used for each type of residue.
** '''Element Symbol''' – A different color is used for each element.
** '''Rainbow (Chain)''' - Colors each chain in the colors of rainbow from N-terminus (red) to C-terminus (violet) (or from 5' to 3' in nucleic acids).
** '''Rainbow (Entity)''' - Similar to '''Rainbow (Chain)''', but identical chains are treated as a single longer chain (e.g. in a homodimer).
** '''Uniform Color''' – One selected color is used for the whole '''Visual'''.
* '''Highlight''' – The color in which this '''Visual''' will be temporarily colored when hovering over the '''Visual''' entity in the entity tree. When the cursor is placed on an atom or residue, it will be colored in the same way.
* '''Selection''' – If you create a [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] from this '''Visual''', it will be distinguished from the rest of the '''Visual''' by having this color.
* '''Opacity''' – The level of transparency of the '''Visual'''. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).

Please keep in mind that changing the type of a '''Visual''' will in fact remove the current visual and replace it with a new one, so all changes you have applied to the current '''Visual''' (such as creating a selection from it) will be lost! You can go to the superior entity and create a new '''Visual''' besides the current '''Visual'''.

 
==Density Visual (VDD)==

[[File:LiteMol-density_visual.png | thumb | 250px | right| Density isosurface at 1.5 σ (2Fo-Fc). ]]

Represents an isosurface of electron density, i.e. the surface in 3D connecting all the points with the value of electron density equal to a specified isovalue.

Applicable actions:
* '''Update Surface''' – Allows you to change the attributes of the visualization.

List of attributes:
* '''Iso value''' – The isovalue of electron density used for the visualized surface.
* '''Relative''' - Indicates whether normalized ('''Relative''' = On) or unnormalized ('''Relative''' = Off) density values are used. The relationship between the two values is as follows: ''Normalized'' = (''Unnormalized'' - ''Mean'') / ''Sigma''.
* '''Color''' – The color of the surface.
* '''Opacity''' – The level of transparency of the surface. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).
* '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).

 
==Interactive Surface (BIS)==

[[File:LiteMol-interactive_surface.png | thumb | 250px | right| Interactive density isosurface at 1.5 σ (2Fo-Fc) shown for a tryptophan residue and its surroundings with radius 2 Angstroms. ]]

This is a visualization of an isosurface of electron density, just as [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]]. The difference is that this surface is shown only when you click on a residue or an atom in the structure. The surface is shown only for the region around the selected residue or atom. An advantage of this interactive visualization is that the relevant region of density surface is not hindered by the rest of the molecule.

Three default '''Interactive Surfaces''' are created automatically when loading density data: blue surface corresponds to isovalue 1.5 in 2Fo-Fc density map. Green and red surfaces correspond to isovalues +3 and -3 in Fo-Fc density map.

Applicable actions:
* '''Update Interactive Surface''' – Change the attributes of the visualization. These attributes are the same as in the case of [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity. An extra attribute is '''Radius''', which allows you to change the size of the region for which the isosurface is shown. Attribute '''Show''' toggles between interactive visualization around the selected region ('''Show''' = Around Selection) and static visualization of the whole map ('''Show''' = Everything, practically equivalent to [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity).

 
=Annotations=

This section describes entities which can store additional information about the structures, such as validation issues or sequence annotations.

==Validation Report (VR)==

[[File:LiteMol-validation_report.png | thumb | 250px | right| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]

[[File:LiteMol-ligand_validation_report.png | thumb | 250px | right| An oligosaccharide in the structure of ribosom-inactivating protein abrin-a (1ABR) colored by the '''Ligand Validation Report'''. The right-most residue is missing an atom. One of the residues in the center has an atom with wrongly annotated chirality. ]]

Represents validation data for this molecule from PDBe. The full validation report in PDF can be downloaded from the [http://www.ebi.ac.uk/pdbe/ PDBe site] (find your molecule, click ''Details'' in ''Experiments and Validation'' section, and then ''Full Validation Report'' in the right panel). An example of a validation report is available [http://www.ebi.ac.uk/pdbe/entry-files/download/1rtc_full_validation.pdf here].

Another type of '''Validation Report''' entity is '''Ligand Validation Report''', which represents validation data for the ligands in this molecule. This data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB].

Applicable actions:
* '''Apply Coloring''' – The structure will be colored according the validation data. For '''PDBe Validation Report''' the color of each residue depends on the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2, and red = 3 or more. For '''Ligand Validation Report''' the residues with missing atoms are colored in red. Also the atoms with wrong chirality are shown in red (examples can be found in PDB entry 1ABR). The correct residues are shown in green.

 
==Sequence Annotations (SA)==

[[File:LiteMol-annotation.png | thumb | 250px | right| Structure of ricin A chain (4Q2V). The orange color indicates the part annotated as ''Ribosome-inactivating protein, subdomain 1'' by InterPro database. ]]

Represents a collection of sequence annotations from PDBe, grouped by the source database.

==Sequence Annotation (SA)==

Represents a single sequence annotation, i.e. assignment of a name to a part of the structure. When you hover above this entity or click on it, the corresponding part of the structure will be shown in a distinctive color.

Applicable actions:
* '''Update PDBe Sequence Annotation''' – Allows you to change the color used for this part of the structure.

 
=Raw Data=

This section contains entities that store data from a file, no matter what these data represent and how their are encoded (i.e. original data from a file before they are parsed). The user will encounter them mostly when loading files from a disk or a URL.

==String Data (SD)==
This entity represents data loaded from a file in textual format (e.g. mmCIF file or PDB file).

Applicable actions:
* '''Molecule''' – Treats the data as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. Make sure to select the appropriate format.
* '''Density Data''' – Treats the data as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity.
* '''CIF Dictionary''' – Treats the data as a CIF dictionary and creates a [[LiteMol:Hierarchy#CIF Dictionary (CD) | CIF Dictionary]] entity. CIF dictionary itself can contain various kinds of data, including molecular structures or density maps.

==Binary Data (BD)==
This entity represents data loaded from a binary file (not human-readable, e.g. [https://github.com/dsehnal/BinaryCIF BinaryCIF] file or CCP4 density file). '''Binary Data''' provides exactly the same actions as [[LiteMol:Hierarchy#String Data (SD) | String Data]].

==CIF Dictionary (CD)==
This entity represents data encoded in a CIF dictionary, which is a flexible format for various kinds of data, so it can contain molecular structures or density maps. A single CIF dictionary can even contain multiple objects (e.g. two density maps: 2Fo-Fc and Fo-Fc).

Applicable actions:
* '''Molecule''' – Treats the data in the '''CIF dictionary''' as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').
* '''Density Data''' – Treats the data in the '''CIF dictionary''' as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').

LiteMol:Hierarchy

2017-05-05T06:00:59Z

Matthew: /* Molecule (M) */

[[File:LiteMol-hierarchy.png | thumb | 200px | right| An example of an '''entity tree'''. ]]

All data in LiteMol are organized in a hierarchy represented by the '''entity tree'''. This tree is shown in LiteMol's left panel. When you click on an entity in the tree, you will see all actions applicable to this entity listed in the right panel.

This page lists all types of entities and explains the actions they provide. The entity types can be divided into four sections: Structures, Visualization, Annotations, and Raw Data.

=Structures=

This section describes the entities used for representation of molecular models and electron density maps. It does not contain any information about how these data are visualized.

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set:
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file.
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action.
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.

==Molecule (M)==

A '''Molecule''' entity represents a set of structural data for a '''Molecule''' (which corresponds to one PDB entry or one mmCIF file).

Applicable actions:
* '''Model''' – Creates a model of the molecule ([[LiteMol:Hierarchy#Molecule Model (MM) |Molecule Model]] entity). Some PDB entries (mostly NMR structures) contain multiple models, in such case, the sequential number ('''Index''') of the desired model to be displayed can be specified.
* '''Density Streaming''' - Creates a [[LiteMol:Hierarchy#Density Streaming (BDS) |Density Streaming]] for this molecule. Clicking on an atom or residue in the structure will instantly download and display the density data for the surrounding region. This solution is, in general, much faster than downloading the whole density map (often more than 1 GB). More details are available [http://webchem.ncbr.muni.cz/DensityServer here].
* '''PDBe Validation Report''' – Downloads wwPDB validation data for this molecule from PDBe and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''Ligand Validation Report''' - Downloads validation data for the ligands in this molecule from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB] and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''PDBe Sequence Annotations''' – Downloads sequence annotation data for this molecule from PDBe (collected from sources such as UniProt, InterProt, Pfam etc.) and creates a [[LiteMol:Hierarchy#Sequence Annotations (SA) | Sequence Annotations]] entity.

==Molecule Model (MM)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create a biological assembly (e.g. a virus capsid). Alternatively, just a part of the model can constitute a biological assembly (e.g. the model contains a dimer while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the biological assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstroms) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for NMR structures.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. As opposed to '''Macromolecule Visual''', this option is less automatic but more flexible. Type, coloring, and other attributes of created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding will be downloaded instantly. This can be usefull when a part of the structure has already been dowloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains in the binding site).
* '''Update Model''' – Applicable when multiple models are included in this PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with specified index. Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model besides the current model.

 
==Group (G)==

This type of entity is merely used to organize multiple entities that are logically connected. An example is a group of selections containing different parts of a model (protein, ligand, and water) or a group of sequence annotations obtained from the same database.

==Molecule Model Selection (SM)==

This is an entity representing a subset of a molecule model. An example is one protein chain, one atom, or a set of all alanine residues. A selection can be created from either a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] entity or a [[LiteMol:Hierarchy#Molecule Visual (VM) | Molecule Visual]] entity. Selections are created using [[LiteMol:SelectionAlgebra | selection algebra language]].

Applicable actions:
* '''Visual''' – Create a visual representation of this selection. Type, coloring, and other attributes of created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Update Selection''' - Change the name of the [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] or change its definition using [[LiteMol:SelectionAlgebra | selection algebra language]]. (This action may not be not available for automatically generated selections.)

==Density Data (DD)==

Represents a three-dimensional map of electron density. Two types of maps are available for most crystal structures: '''2Fo-Fc''' and '''Fo-Fc'''. Only one map is available for cryo-EM structures.

Applicable actions:
* '''Surface''' – Creates a visualization of the density isosurface with given isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) |Density Visual]] entity).
* '''Interactive Surface''' – Creates a density isosurface which is shown only for a region of the molecule when you click on that region ([[LiteMol:Hierarchy#Interactive Surface (BIS) |Interactive Surface]] entity).
* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.

=Visualization=

This section contains entities that represent different visualizations of molecules and electron density maps.

==Molecule Visual (VM)==

[[File:LiteMol-cartoon.png | thumb | 250px | right| '''Cartoon''' visual for 1CBS. ]]

[[File:LiteMol-CA_trace.png | thumb | 250px | right| '''C-α trace''' visual for 1CBS. ]]

[[File:LiteMol-balls_and_sticks.png | thumb | 250px | right| '''Balls and Sticks''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-VDW_balls.png | thumb | 250px | right| '''VDW Balls''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-surface.png | thumb | 250px | right| '''Surface''' visual for 1CBS. ]]

A '''Molecule Visual''' is simply a visualization of a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] or its part. It is defined mostly by its type and coloring. These can be changed in '''Update Visual''' action. Click on the “+” icon next to “Type” or “Coloring” to modify other attributes. Some attributes are only available for certain types of visualization.

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Update Visual''' – Allows you to change the type of visualization and other attributes.

List of attributes:
* '''Type''' – One of the following:
** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, sheets, and unstructured regions.
** '''C-α Trace''' – Simplified wire-like representation of the backbone (no side-chains).
** '''Balls and Sticks''' – Atoms are represented by balls, bonds are shown as sticks connecting them. Keep in mind that most structures from X-ray and cryo-EM experiments do not provide positions of hydrogen atoms, so these are not visible in '''Ball and Sticks''' representation. There are some extra attributes that you can modify:
*** '''VDW''' – Indicates whether all atoms are shown as balls with uniform radius ('''VDW''' = Off) or ball's radius is based on the element's van der Waals radius ('''VDW''' = On).
*** '''Scale''' – (Only when '''VDW''' = On) The ratio between the ball's radius and the element's van der Waals radius.
*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the balls in Angstroms.
*** '''Bond Rds''' – The width (radius) of the sticks.
*** '''Bond''' – Color of the sticks.
** '''VDW Balls''' – Shows atoms as balls width radii corresponding to their van der Waals radii.
** '''Surface''' – Shows the smoothed boundary surface of the space “filled” by the molecule. There are some extra attributes that you can modify:
*** '''Probe Radius''' – How much space around an atom is considered as “filled” by this atom.
*** '''Smoothing''' – With lower values curvature of the surface around individual atoms will be more noticeable. With higher values the surface will be smoother.
*** '''Auto Detail''' - If set to On, the optimal level of detail is automatically derived from the size of the molecule. If set to Off, the level of detail can be adjusted manually (see the next item).
*** '''Detail''' – Defines how precisely the surface should be visualized. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource-demanding) when visualizing larger molecules.
*** '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).
* '''Detail''' – Defines how precisely the molecule should be visualized and can range from '''Very Low''' to '''Very High'''. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource-demanding) when visualizing larger molecules. If you choose '''Automatic''', LiteMol will infer the optimal level of detail from the molecule's size.
* '''Coloring''' – One of the following:
** '''Chain ID''' – Every chain will be shown in a different color.
** '''Entity ID''' – The same as '''Chain ID''' but identical chains are shown in the same color.
** '''Entity Type''' – Every type of entity (polymer, non-polymer, water) is shown in a different color.
** '''Residue Name''' – A different color is used for each type of residue.
** '''Element Symbol''' – A different color is used for each element.
** '''Rainbow (Chain)''' - Colors each chain in the colors of rainbow from N-terminus (red) to C-terminus (violet) (or from 5' to 3' in nucleic acids).
** '''Rainbow (Entity)''' - Similar to '''Rainbow (Chain)''', but identical chains are treated as a single longer chain (e.g. in a homodimer).
** '''Uniform Color''' – One selected color is used for the whole '''Visual'''.
* '''Highlight''' – The color in which this '''Visual''' will be temporarily colored when hovering over the '''Visual''' entity in the entity tree. When the cursor is placed on an atom or residue, it will be colored in the same way.
* '''Selection''' – If you create a [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] from this '''Visual''', it will be distinguished from the rest of the '''Visual''' by having this color.
* '''Opacity''' – The level of transparency of the '''Visual'''. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).

Please keep in mind that changing the type of a '''Visual''' will in fact remove the current visual and replace it with a new one, so all changes you have applied to the current '''Visual''' (such as creating a selection from it) will be lost! You can go to the superior entity and create a new '''Visual''' besides the current '''Visual'''.

 
==Density Visual (VDD)==

[[File:LiteMol-density_visual.png | thumb | 250px | right| Density isosurface at 1.5 σ (2Fo-Fc). ]]

Represents an isosurface of electron density, i.e. the surface in 3D connecting all the points with the value of electron density equal to a specified isovalue.

Applicable actions:
* '''Update Surface''' – Allows you to change the attributes of the visualization.

List of attributes:
* '''Iso value''' – The isovalue of electron density used for the visualized surface.
* '''Relative''' - Indicates whether normalized ('''Relative''' = On) or unnormalized ('''Relative''' = Off) density values are used. The relationship between the two values is as follows: ''Normalized'' = (''Unnormalized'' - ''Mean'') / ''Sigma''.
* '''Color''' – The color of the surface.
* '''Opacity''' – The level of transparency of the surface. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).
* '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).

 
==Interactive Surface (BIS)==

[[File:LiteMol-interactive_surface.png | thumb | 250px | right| Interactive density isosurface at 1.5 σ (2Fo-Fc) shown for a tryptophan residue and its surroundings with radius 2 Angstroms. ]]

This is a visualization of an isosurface of electron density, just as [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]]. The difference is that this surface is shown only when you click on a residue or an atom in the structure. The surface is shown only for the region around the selected residue or atom. An advantage of this interactive visualization is that the relevant region of density surface is not hindered by the rest of the molecule.

Three default '''Interactive Surfaces''' are created automatically when loading density data: blue surface corresponds to isovalue 1.5 in 2Fo-Fc density map. Green and red surfaces correspond to isovalues +3 and -3 in Fo-Fc density map.

Applicable actions:
* '''Update Interactive Surface''' – Change the attributes of the visualization. These attributes are the same as in the case of [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity. An extra attribute is '''Radius''', which allows you to change the size of the region for which the isosurface is shown. Attribute '''Show''' toggles between interactive visualization around the selected region ('''Show''' = Around Selection) and static visualization of the whole map ('''Show''' = Everything, practically equivalent to [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity).

 
=Annotations=

This section describes entities which can store additional information about the structures, such as validation issues or sequence annotations.

==Validation Report (VR)==

[[File:LiteMol-validation_report.png | thumb | 250px | right| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]

[[File:LiteMol-ligand_validation_report.png | thumb | 250px | right| An oligosaccharide in the structure of ribosom-inactivating protein abrin-a (1ABR) colored by the '''Ligand Validation Report'''. The right-most residue is missing an atom. One of the residues in the center has an atom with wrongly annotated chirality. ]]

Represents validation data for this molecule from PDBe. The full validation report in PDF can be downloaded from the [http://www.ebi.ac.uk/pdbe/ PDBe site] (find your molecule, click ''Details'' in ''Experiments and Validation'' section, and then ''Full Validation Report'' in the right panel). An example of a validation report is available [http://www.ebi.ac.uk/pdbe/entry-files/download/1rtc_full_validation.pdf here].

Another type of '''Validation Report''' entity is '''Ligand Validation Report''', which represents validation data for the ligands in this molecule. This data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB].

Applicable actions:
* '''Apply Coloring''' – The structure will be colored according the validation data. For '''PDBe Validation Report''' the color of each residue depends on the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2, and red = 3 or more. For '''Ligand Validation Report''' the residues with missing atoms are colored in red. Also the atoms with wrong chirality are shown in red (examples can be found in PDB entry 1ABR). The correct residues are shown in green.

 
==Sequence Annotations (SA)==

[[File:LiteMol-annotation.png | thumb | 250px | right| Structure of ricin A chain (4Q2V). The orange color indicates the part annotated as ''Ribosome-inactivating protein, subdomain 1'' by InterPro database. ]]

Represents a collection of sequence annotations from PDBe, grouped by the source database.

==Sequence Annotation (SA)==

Represents a single sequence annotation, i.e. assignment of a name to a part of the structure. When you hover above this entity or click on it, the corresponding part of the structure will be shown in a distinctive color.

Applicable actions:
* '''Update PDBe Sequence Annotation''' – Allows you to change the color used for this part of the structure.

 
=Raw Data=

This section contains entities that store data from a file, no matter what these data represent and how their are encoded (i.e. original data from a file before they are parsed). The user will encounter them mostly when loading files from a disk or a URL.

==String Data (SD)==
This entity represents data loaded from a file in textual format (e.g. mmCIF file or PDB file).

Applicable actions:
* '''Molecule''' – Treats the data as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. Make sure to select the appropriate format.
* '''Density Data''' – Treats the data as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity.
* '''CIF Dictionary''' – Treats the data as a CIF dictionary and creates a [[LiteMol:Hierarchy#CIF Dictionary (CD) | CIF Dictionary]] entity. CIF dictionary itself can contain various kinds of data, including molecular structures or density maps.

==Binary Data (BD)==
This entity represents data loaded from a binary file (not human-readable, e.g. [https://github.com/dsehnal/BinaryCIF BinaryCIF] file or CCP4 density file). '''Binary Data''' provides exactly the same actions as [[LiteMol:Hierarchy#String Data (SD) | String Data]].

==CIF Dictionary (CD)==
This entity represents data encoded in a CIF dictionary, which is a flexible format for various kinds of data, so it can contain molecular structures or density maps. A single CIF dictionary can even contain multiple objects (e.g. two density maps: 2Fo-Fc and Fo-Fc).

Applicable actions:
* '''Molecule''' – Treats the data in the '''CIF dictionary''' as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').
* '''Density Data''' – Treats the data in the '''CIF dictionary''' as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').

LiteMol:Hierarchy

2017-05-04T21:57:17Z

Matthew: edited by MJC to Molecule model

[[File:LiteMol-hierarchy.png | thumb | 200px | right| An example of an '''entity tree'''. ]]

All data in LiteMol are organized in a hierarchy represented by the '''entity tree'''. This tree is shown in LiteMol's left panel. When you click on an entity in the tree, you will see all actions applicable to this entity listed in the right panel.

This page lists all types of entities and explains the actions they provide. The entity types can be divided into four sections: Structures, Visualization, Annotations, and Raw Data.

=Structures=

This section describes the entities used for representation of molecular models and electron density maps. It does not contain any information about how these data are visualized.

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set:
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file.
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action.
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.

==Molecule (M)==

A '''Molecule''' entity represents a set of structural data for a '''Molecule''' which corresponds to one PDB entry or one mmCIF file).

Applicable actions:
* '''Model''' – Creates a model of the molecule ([[LiteMol:Hierarchy#Molecule Model (MM) |Molecule Model]] entity). Some PDB entries (mostly NMR structures) contain multiple models, in such case, the sequential number ('''Index''') of the desired model to be displayed can be specified.
* '''Density Streaming''' - Creates a [[LiteMol:Hierarchy#Density Streaming (BDS) |Density Streaming]] for this molecule. Clicking on an atom or residue in the structure will instantly download and display the density data for the surrounding region. This solution is, in general, much faster than downloading the whole density map (often more than 1 GB). More details are available [http://webchem.ncbr.muni.cz/DensityServer here].
* '''PDBe Validation Report''' – Downloads wwPDB validation data for this molecule from PDBe and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''Ligand Validation Report''' - Downloads validation data for the ligands in this molecule from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB] and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''PDBe Sequence Annotations''' – Downloads sequence annotation data for this molecule from PDBe (collected from sources such as UniProt, InterProt, Pfam etc.) and creates a [[LiteMol:Hierarchy#Sequence Annotations (SA) | Sequence Annotations]] entity.

==Molecule Model (MM)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create a biological assembly (e.g. a virus capsid). Alternatively, just a part of the model can constitute a biological assembly (e.g. the model contains a dimer while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the biological assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstroms) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for NMR structures.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. As opposed to '''Macromolecule Visual''', this option is less automatic but more flexible. Type, coloring, and other attributes of created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding will be downloaded instantly. This can be usefull when a part of the structure has already been dowloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains in the binding site).
* '''Update Model''' – Applicable when multiple models are included in this PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with specified index. Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model besides the current model.

 
==Group (G)==

This type of entity is merely used to organize multiple entities that are logically connected. An example is a group of selections containing different parts of a model (protein, ligand, and water) or a group of sequence annotations obtained from the same database.

==Molecule Model Selection (SM)==

This is an entity representing a subset of a molecule model. An example is one protein chain, one atom, or a set of all alanine residues. A selection can be created from either a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] entity or a [[LiteMol:Hierarchy#Molecule Visual (VM) | Molecule Visual]] entity. Selections are created using [[LiteMol:SelectionAlgebra | selection algebra language]].

Applicable actions:
* '''Visual''' – Create a visual representation of this selection. Type, coloring, and other attributes of created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Update Selection''' - Change the name of the [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] or change its definition using [[LiteMol:SelectionAlgebra | selection algebra language]]. (This action may not be not available for automatically generated selections.)

==Density Data (DD)==

Represents a three-dimensional map of electron density. Two types of maps are available for most crystal structures: '''2Fo-Fc''' and '''Fo-Fc'''. Only one map is available for cryo-EM structures.

Applicable actions:
* '''Surface''' – Creates a visualization of the density isosurface with given isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) |Density Visual]] entity).
* '''Interactive Surface''' – Creates a density isosurface which is shown only for a region of the molecule when you click on that region ([[LiteMol:Hierarchy#Interactive Surface (BIS) |Interactive Surface]] entity).
* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.

=Visualization=

This section contains entities that represent different visualizations of molecules and electron density maps.

==Molecule Visual (VM)==

[[File:LiteMol-cartoon.png | thumb | 250px | right| '''Cartoon''' visual for 1CBS. ]]

[[File:LiteMol-CA_trace.png | thumb | 250px | right| '''C-α trace''' visual for 1CBS. ]]

[[File:LiteMol-balls_and_sticks.png | thumb | 250px | right| '''Balls and Sticks''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-VDW_balls.png | thumb | 250px | right| '''VDW Balls''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-surface.png | thumb | 250px | right| '''Surface''' visual for 1CBS. ]]

A '''Molecule Visual''' is simply a visualization of a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] or its part. It is defined mostly by its type and coloring. These can be changed in '''Update Visual''' action. Click on the “+” icon next to “Type” or “Coloring” to modify other attributes. Some attributes are only available for certain types of visualization.

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Update Visual''' – Allows you to change the type of visualization and other attributes.

List of attributes:
* '''Type''' – One of the following:
** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, sheets, and unstructured regions.
** '''C-α Trace''' – Simplified wire-like representation of the backbone (no side-chains).
** '''Balls and Sticks''' – Atoms are represented by balls, bonds are shown as sticks connecting them. Keep in mind that most structures from X-ray and cryo-EM experiments do not provide positions of hydrogen atoms, so these are not visible in '''Ball and Sticks''' representation. There are some extra attributes that you can modify:
*** '''VDW''' – Indicates whether all atoms are shown as balls with uniform radius ('''VDW''' = Off) or ball's radius is based on the element's van der Waals radius ('''VDW''' = On).
*** '''Scale''' – (Only when '''VDW''' = On) The ratio between the ball's radius and the element's van der Waals radius.
*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the balls in Angstroms.
*** '''Bond Rds''' – The width (radius) of the sticks.
*** '''Bond''' – Color of the sticks.
** '''VDW Balls''' – Shows atoms as balls width radii corresponding to their van der Waals radii.
** '''Surface''' – Shows the smoothed boundary surface of the space “filled” by the molecule. There are some extra attributes that you can modify:
*** '''Probe Radius''' – How much space around an atom is considered as “filled” by this atom.
*** '''Smoothing''' – With lower values curvature of the surface around individual atoms will be more noticeable. With higher values the surface will be smoother.
*** '''Auto Detail''' - If set to On, the optimal level of detail is automatically derived from the size of the molecule. If set to Off, the level of detail can be adjusted manually (see the next item).
*** '''Detail''' – Defines how precisely the surface should be visualized. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource-demanding) when visualizing larger molecules.
*** '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).
* '''Detail''' – Defines how precisely the molecule should be visualized and can range from '''Very Low''' to '''Very High'''. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource-demanding) when visualizing larger molecules. If you choose '''Automatic''', LiteMol will infer the optimal level of detail from the molecule's size.
* '''Coloring''' – One of the following:
** '''Chain ID''' – Every chain will be shown in a different color.
** '''Entity ID''' – The same as '''Chain ID''' but identical chains are shown in the same color.
** '''Entity Type''' – Every type of entity (polymer, non-polymer, water) is shown in a different color.
** '''Residue Name''' – A different color is used for each type of residue.
** '''Element Symbol''' – A different color is used for each element.
** '''Rainbow (Chain)''' - Colors each chain in the colors of rainbow from N-terminus (red) to C-terminus (violet) (or from 5' to 3' in nucleic acids).
** '''Rainbow (Entity)''' - Similar to '''Rainbow (Chain)''', but identical chains are treated as a single longer chain (e.g. in a homodimer).
** '''Uniform Color''' – One selected color is used for the whole '''Visual'''.
* '''Highlight''' – The color in which this '''Visual''' will be temporarily colored when hovering over the '''Visual''' entity in the entity tree. When the cursor is placed on an atom or residue, it will be colored in the same way.
* '''Selection''' – If you create a [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] from this '''Visual''', it will be distinguished from the rest of the '''Visual''' by having this color.
* '''Opacity''' – The level of transparency of the '''Visual'''. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).

Please keep in mind that changing the type of a '''Visual''' will in fact remove the current visual and replace it with a new one, so all changes you have applied to the current '''Visual''' (such as creating a selection from it) will be lost! You can go to the superior entity and create a new '''Visual''' besides the current '''Visual'''.

 
==Density Visual (VDD)==

[[File:LiteMol-density_visual.png | thumb | 250px | right| Density isosurface at 1.5 σ (2Fo-Fc). ]]

Represents an isosurface of electron density, i.e. the surface in 3D connecting all the points with the value of electron density equal to a specified isovalue.

Applicable actions:
* '''Update Surface''' – Allows you to change the attributes of the visualization.

List of attributes:
* '''Iso value''' – The isovalue of electron density used for the visualized surface.
* '''Relative''' - Indicates whether normalized ('''Relative''' = On) or unnormalized ('''Relative''' = Off) density values are used. The relationship between the two values is as follows: ''Normalized'' = (''Unnormalized'' - ''Mean'') / ''Sigma''.
* '''Color''' – The color of the surface.
* '''Opacity''' – The level of transparency of the surface. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).
* '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).

 
==Interactive Surface (BIS)==

[[File:LiteMol-interactive_surface.png | thumb | 250px | right| Interactive density isosurface at 1.5 σ (2Fo-Fc) shown for a tryptophan residue and its surroundings with radius 2 Angstroms. ]]

This is a visualization of an isosurface of electron density, just as [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]]. The difference is that this surface is shown only when you click on a residue or an atom in the structure. The surface is shown only for the region around the selected residue or atom. An advantage of this interactive visualization is that the relevant region of density surface is not hindered by the rest of the molecule.

Three default '''Interactive Surfaces''' are created automatically when loading density data: blue surface corresponds to isovalue 1.5 in 2Fo-Fc density map. Green and red surfaces correspond to isovalues +3 and -3 in Fo-Fc density map.

Applicable actions:
* '''Update Interactive Surface''' – Change the attributes of the visualization. These attributes are the same as in the case of [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity. An extra attribute is '''Radius''', which allows you to change the size of the region for which the isosurface is shown. Attribute '''Show''' toggles between interactive visualization around the selected region ('''Show''' = Around Selection) and static visualization of the whole map ('''Show''' = Everything, practically equivalent to [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity).

 
=Annotations=

This section describes entities which can store additional information about the structures, such as validation issues or sequence annotations.

==Validation Report (VR)==

[[File:LiteMol-validation_report.png | thumb | 250px | right| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]

[[File:LiteMol-ligand_validation_report.png | thumb | 250px | right| An oligosaccharide in the structure of ribosom-inactivating protein abrin-a (1ABR) colored by the '''Ligand Validation Report'''. The right-most residue is missing an atom. One of the residues in the center has an atom with wrongly annotated chirality. ]]

Represents validation data for this molecule from PDBe. The full validation report in PDF can be downloaded from the [http://www.ebi.ac.uk/pdbe/ PDBe site] (find your molecule, click ''Details'' in ''Experiments and Validation'' section, and then ''Full Validation Report'' in the right panel). An example of a validation report is available [http://www.ebi.ac.uk/pdbe/entry-files/download/1rtc_full_validation.pdf here].

Another type of '''Validation Report''' entity is '''Ligand Validation Report''', which represents validation data for the ligands in this molecule. This data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB].

Applicable actions:
* '''Apply Coloring''' – The structure will be colored according the validation data. For '''PDBe Validation Report''' the color of each residue depends on the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2, and red = 3 or more. For '''Ligand Validation Report''' the residues with missing atoms are colored in red. Also the atoms with wrong chirality are shown in red (examples can be found in PDB entry 1ABR). The correct residues are shown in green.

 
==Sequence Annotations (SA)==

[[File:LiteMol-annotation.png | thumb | 250px | right| Structure of ricin A chain (4Q2V). The orange color indicates the part annotated as ''Ribosome-inactivating protein, subdomain 1'' by InterPro database. ]]

Represents a collection of sequence annotations from PDBe, grouped by the source database.

==Sequence Annotation (SA)==

Represents a single sequence annotation, i.e. assignment of a name to a part of the structure. When you hover above this entity or click on it, the corresponding part of the structure will be shown in a distinctive color.

Applicable actions:
* '''Update PDBe Sequence Annotation''' – Allows you to change the color used for this part of the structure.

 
=Raw Data=

This section contains entities that store data from a file, no matter what these data represent and how their are encoded (i.e. original data from a file before they are parsed). The user will encounter them mostly when loading files from a disk or a URL.

==String Data (SD)==
This entity represents data loaded from a file in textual format (e.g. mmCIF file or PDB file).

Applicable actions:
* '''Molecule''' – Treats the data as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. Make sure to select the appropriate format.
* '''Density Data''' – Treats the data as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity.
* '''CIF Dictionary''' – Treats the data as a CIF dictionary and creates a [[LiteMol:Hierarchy#CIF Dictionary (CD) | CIF Dictionary]] entity. CIF dictionary itself can contain various kinds of data, including molecular structures or density maps.

==Binary Data (BD)==
This entity represents data loaded from a binary file (not human-readable, e.g. [https://github.com/dsehnal/BinaryCIF BinaryCIF] file or CCP4 density file). '''Binary Data''' provides exactly the same actions as [[LiteMol:Hierarchy#String Data (SD) | String Data]].

==CIF Dictionary (CD)==
This entity represents data encoded in a CIF dictionary, which is a flexible format for various kinds of data, so it can contain molecular structures or density maps. A single CIF dictionary can even contain multiple objects (e.g. two density maps: 2Fo-Fc and Fo-Fc).

Applicable actions:
* '''Molecule''' – Treats the data in the '''CIF dictionary''' as a representation of a molecular structure and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').
* '''Density Data''' – Treats the data in the '''CIF dictionary''' as an electron density map and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. As the dictionary may contain multiple objects, one of them must be selected explicitly (parameter '''Source''').

LiteMol:Functionality

2017-05-04T20:51:58Z

Matthew: /* Advanced features */ edited mjc

{{large| '''LiteMol is a powerful and blazing-fast cross-platform tool for handling 3D macromolecular data in the browser. [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ Try it now!]'''}}

=Classic features=
* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).
* All common visualization models ('balls-n-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).
* Displays electron densities for X-ray crystallographic structures and electric potential maps for cryo-EM models.
* Available as a [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ standalone viewer] or as a [https://github.com/dsehnal/LiteMol library} for embedding into third party applications.

[[Image:LiteMol-Models.png|center|800px]]

=Advanced features=
* Introduces the [https://github.com/dsehnal/BinaryCIF BinaryCIF] a compression format compatible with standard PDBx/mmCIF format ''greatly reducing'' the amount of transferred data.
* [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] allows for streaming only those parts of the structural model relevant for the user required visualization. This further ''decreases'' the amount of ''transferred data'' and facilitates ''near instant responsiveness'' even for huge structures such as ribosomes and viral capsids. All in your web browser.
* [http://webchem.ncbr.muni.cz/DensityServer DensityServer ] allows ''instant access'' to full resolution user determined slices of ''electron density'' (e.g. binding sites) and down sampled surface of the entire biomacromolecular structure.
* Displays [https://www.wwpdb.org/validation/validation-reports wwPDB validation reports] and [[ValidatorDB:UserManual | ValidatorDB ligand validation]].
* Displays ''sequence annotations'' from [http://pfam.xfam.org/ Pfam], [https://www.ebi.ac.uk/interpro/ InterPro], [www.cathdb.info CATH], [http://scop.berkeley.edu/ SCOP], [http://www.uniprot.org/ UniProt].
* Visualizer requires only an up-to-date ''web browser'' with no dependencies required. Runs on all ''mobile devices''.
* Minimal ''memory footprint''.

[[Image:LiteMol-Performance.png|center|800px]]

LiteMol:Functionality

2017-05-04T20:47:54Z

Matthew: edited by MJC

{{large| '''LiteMol is a powerful and blazing-fast cross-platform tool for handling 3D macromolecular data in the browser. [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ Try it now!]'''}}

=Classic features=
* Supports all major structural data formats ([http://mmcif.wwpdb.org/ PDBx/mmcif], [https://www.wwpdb.org/documentation/file-format PDB], [http://pubs.acs.org/doi/pdf/10.1021/ci00007a012 SDF]).
* All common visualization models ('balls-n-sticks'/cartoon/Cα-trace/VDW spheres/surfaces).
* Displays electron densities for X-ray crystallographic structures and electric potential maps for cryo-EM models.
* Available as a [https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/ standalone viewer] or as a [https://github.com/dsehnal/LiteMol library} for embedding into third party applications.

[[Image:LiteMol-Models.png|center|800px]]

=Advanced features=
* Introduces the [https://github.com/dsehnal/BinaryCIF BinaryCIF] a compression format compatible with standard PDBx/mmCIF format ''greatly reducing'' amount of transferred data.
* [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] allows for streaming only parts of the structure models relevant for user deemed visualization. This further ''decreases'' the amount of ''transferred data'' and facilitates ''near instant responsiveness'' even for huge structures like ribosomes and viral capsids. All in your web browser.
* [http://webchem.ncbr.muni.cz/DensityServer DensityServer ] allows ''instant access'' to full resolution user deemed slices of ''electron density'' (e.g. binding sites) and down sampled surface of the entire biomacromolecular structure.
* Displays [https://www.wwpdb.org/validation/validation-reports PDB validation reports] and [[ValidatorDB:UserManual | ValidatorDB ligand validation]].
* Displays ''sequence annotations'' from [http://pfam.xfam.org/ Pfam], [https://www.ebi.ac.uk/interpro/ InterPro], [www.cathdb.info CATH], [http://scop.berkeley.edu/ SCOP], [http://www.uniprot.org/ UniProt].
* Visualizer which requires only an up to date ''web browser'' with no dependencies needed. Runs on all ''mobile devices''.
* Minimal ''memory footprint''.

[[Image:LiteMol-Performance.png|center|800px]]

LiteMol:Introduction

2017-05-04T20:25:21Z

Matthew: edited by MJC NB goto add_web_address

__NOTOC__

Visualization of protein and nucleic acid structures is an essential task in structural biology. A variety of visualization tools are available which all differ in functionality and manner of use. Many can be limited by the size of some structures, unable to render the larger complexes in structural archives. Moreover, their use is often troublesome because of installation, system requirements, or licence purchase.

=What is LiteMol?=

LiteMol is a visualization tool designed to be user-friendly yet flexible, interactive, and very fast even for extremely large protein structures. LiteMol can be run directly from your web browser without any installation and it does not require any plugins. It can be incorporated as an applet in any web page.

Unlike many visualizers, LiteMol can display extremely large structures containing millions of atoms quickly. Even structures such as virus capsids can be shown in a few seconds. The degree of detail can be adjusted from rather coarse (but fast) to very smooth (though slower).

LiteMol provides the standard functionality expected of a molecular visualizer such as different representations (cartoon, balls and sticks, Van der Waals spheres, surface, C-α trace), selecting substructures using a simple query language, coloring the parts of the structure etc.

Apart from the atomic models, LiteMol can be used to display electron densities (for X-ray crystallographic data) and cryo-EM data. The validation data from wwPDB validation reports (via the PDBe API) as well as annotation data from several databases are available and can be mapped to the 3D structure and shown as distinctive coloring.
Another feature of LiteMol is its extended interactivity. Interesting regions of the structure can be inspected in more detail by a single click.

Data can be uploaded from a CIF file stored locally or downloaded directly from PDBe by entering the PDB ID. Larger structures can also be accessed efficiently using Coordinate Streaming, so the essential data are downloaded immediately and the rest of the data are fetched only when needed, limiting download sizes of files.

=How to use LiteMol?=

# Go to [http://add_web_address LiteMol's web page].
# Find “Molecule from PDBe” in the right panel, enter the PDB identifier (such as 1CBS) of your molecule, and click “Add”.
# Your molecule has been downloaded from the server and should be visible in the center of the screen.
# Now you can use all the functions. Just click at any entity in the hierarchy displayed in the left panel and all available actions will be shown in the right panel. Find more tips on the page on [[LiteMol:Functionality | functionality]].

LiteMol:UserManual

2017-05-04T19:58:28Z

Matthew: edited by MJC

__NOTOC__
[[File:LiteMol-logo.png | 350px | right]]
'''LiteMol''' is a web tool for visualization of molecular structures, particularly macromolecules. It is designed to be user-friendly yet flexible, interactive, and very fast even for extremely large protein structures. '''LiteMol''' can be run directly from your web browser.

Apart from the standard functionality expected of visualization tools, '''LiteMol''' can visualize electron densities and cryo-EM maps from which the models are derived. It can also display validation and annotation data from several databases on the model.

This user manual provides the necessary information about '''LiteMol's''' functionality and the instructions for its use. It also shows the most typical use cases with step-by-step instructions. Additional hints are available in '''LiteMol''' itself when hovering above the ''i'' icons.

'''LiteMol''' is available from the following address: [https://webchemdev.ncbr.muni.cz/Litemol webchemdev.ncbr.muni.cz/Litemol].

 
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===[[LiteMol:Introduction | Introduction]]===

===[[LiteMol:Hierarchy | Hierarchy of Entities]]===
#[[LiteMol:Hierarchy#Structures| Structures]]
#[[LiteMol:Hierarchy#Visualization| Visualization]]
#[[LiteMol:Hierarchy#Annotations | Annotations]]
#[[LiteMol:Hierarchy#Raw Data | Raw Data]]
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===[[LiteMol:Functionality | Functionality]]===
#[[LiteMol:Functionality#Classic features| Features]]
#[[LiteMol:Functionality#Advanced features| Advanced]]
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===[[LiteMol:SelectionAlgebra | Selection Algebra]]===
#[[LiteMol:SelectionAlgebra#Basic queries| Basic]]
#[[LiteMol:SelectionAlgebra#Advanced queries| Advanced]]
#[[LiteMol:SelectionAlgebra#Logical queries| Logical]]
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===[[LiteMol:Use Cases | Use Cases]]===

===[[LiteMol:Embedding | Embedding in Your Web]]===

===[[LiteMol:Integration | Integration with other services]]===
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