LiteMol:Hierarchy - Revision history

Matthew: /* Raw Data */ mjc

2017-05-05T12:08:42Z

Raw Data: mjc

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	=Raw Data=		=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.		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 (S<sub>D</sub>)==		==String Data (S<sub>D</sub>)==

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

2017-05-05T12:00:10Z

Sequence Annotations (SA): mjc

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


	==Sequence Annotation (SA)==		==Sequence Annotation (SA)==

Matthew: /* Validation Report (VR) */ mjc

2017-05-05T11:59:12Z

Validation Report (VR): mjc

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	[[File:LiteMol-validation_report.png \| thumb \| 250px \| right\| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]		[[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. ]]		[[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 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].		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 ~~molecule~~. ~~This~~ data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB].		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:		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.		* '''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.


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	==Sequence Annotations (SA)==		==Sequence Annotations (SA)==

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

2017-05-05T11:52:39Z

Interactive Surface (BIS): mjc edit

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	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.		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~~.		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:		Applicable actions:
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	=Annotations=		=Annotations=

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

2017-05-05T10:57:04Z

Molecule Visual (VM): mjc edit

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

2017-05-05T10:01:39Z

Density Data (DD): mjc edit

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	==Density Data (DD)==		==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~~.		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:		Applicable actions:
	* '''Surface''' – Creates a visualization of the density isosurface with ~~given~~ isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) \|Density Visual]] entity).		* '''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).		* '''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.		* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.


	=Visualization=		=Visualization=

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

2017-05-05T09:56:18Z

Molecule Model Selection (SM): mjc edit

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	Applicable actions:		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]].		* '''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.)		* '''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)==		==Density Data (DD)==

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

2017-05-05T09:54:03Z

Group (G): mjc edit

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	==Group (G)==		==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.		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 (S<sub>M</sub>)==		==Molecule Model Selection (S<sub>M</sub>)==

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

2017-05-05T09:49:14Z

Molecule Model (MM): mjc edit

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	Applicable actions:		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]].		* '''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.		* '''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 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~~.		* '''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.		* '''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]].		* '''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 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).		* '''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 ~~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.		* '''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.


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	==Group (G)==		==Group (G)==

Matthew: /* Molecule (M) */

2017-05-05T06:00:59Z

Molecule (M)

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	==Molecule (M)==		==Molecule (M)==

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

	Applicable actions:		Applicable actions:
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	* '''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.		* '''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.		* '''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 (M<sub>M</sub>)==		==Molecule Model (M<sub>M</sub>)==

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	List of attributes:		List of attributes:
	* '''Type''' – One of the following:		* '''Type''' – One of the following:
	** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, ~~sheets~~, and unstructured regions.		** '''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).		** '''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:		** '''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).		*** '''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 ~~ball's~~ radius and the element's ~~van~~ der Waals radius.		*** '''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 ~~balls~~ in ~~Angstroms~~.		*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the sphere in Angstrom.
	*** '''Bond Rds''' – The width (radius) of the sticks.		*** '''Bond Rds''' – The width (radius) of the sticks.
	*** '''Bond''' – Color of the sticks.		*** '''Bond''' – Color of the sticks.
	** '''VDW Balls''' – Shows atoms as ~~balls~~ width radii corresponding to their ~~van~~ der Waals radii.		** '''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:		** '''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.		*** '''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.		*** '''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).		*** '''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.		*** '''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).		*** '''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.		* '''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:		* '''Coloring''' – One of the following:
	** '''Chain ID''' – Every chain will be shown in a different color.		** '''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 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.		** '''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.		** '''Residue Name''' – A different color is used for each type of residue.
	** '''Element Symbol''' – A different color is used for each element.		** '''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 (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).		** '''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'''.		** '''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.		* '''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.
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	==Density Visual (V<sub>DD</sub>)==		==Density Visual (V<sub>DD</sub>)==