LiteMol:Hierarchy

All data in LiteMol are organized in a hierarchy represented by 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.

Root Entity

The highest level of the hierarchy is the Root Entity, which is created at the beginning of the 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 from PDBe – Downloads the structure of a molecule specified by its PDB ID from PDBe server and creates a LiteMol:Hierarchy#Molecule entity.
• Density Data from PDBe – Downloads the electron density data for a molecule specified by its PDB ID from PDBe server and creates a Density Data entity. This is applicable only for structures from X-ray diffraction experiments.
• 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, whose full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, 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).
• Molecule from CIF File – Reads the structural data from a file on your computer. The file must be in mmCIF format (.cif). Current version of LiteMol does not support mmCIF files provided by PDBeChem.

The result of any of these actions is creation of a Molecule entity, which is direct descendant of the Root Entity. Other descendants of this Molecule entity are also created automatically.

Molecule (M)

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

Applicable actions:

• Model – Creates a model of the molecule. Some PDB entries contain multiple models (mostly NMR structures). In such case, the sequential number (Index) of desired model can be specified.
• PDBe Validation Report – Downloads validation data for this molecule from PDBe and creates 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 Sequence Annotations entity.

Molecule Model (M_M)

A Molecule Model entity represents a static model of a molecule, i.e. atomic coordinates for 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 Molecule Model Selection entity. Selections are defined using 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 neighbors 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 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 Visual can be specified. Find more about these settings here.
• Coordinate Streaming – will be removed?
• Update Model – Applicable when multiple models are included in this PDB entry. 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 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 (S_M)

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 Molecule Model entity or a Visual entity. Selections are created using selection algebra language.

Applicable actions:

• Visual – Create a visual representation of this selection. Type, coloring, and other attributes of created Visual can be specified. Find more about these settings here.

Molecule Visual (V_M)

A Visual is simply a visualization of a 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.

Applicable actions:

• Selection – Selects a part of the model and creates Molecule Model Selection entity. Selections are defined using 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” with 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.
    • 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.
  • Uniform Color – One selected color is used for the whole Visual.
• Highlight – The color in which this Visual should be temporarily colored when hovering above the Visual entity in the entity tree.
• Selection – If you create a 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. Value 1 means totally opaque whereas 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 selection of it) will be lost! You can go to the superior entity and create a new Visual besides the current Visual. add pictures here!

Validation Report (VR)

Represents Validation data for this molecule from PDBe.

Applicable actions:

• Apply Coloring – Residues will be colored according to 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.

Sequence Annotations (SA)

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.