PDB plugin: Difference between revisions
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Screenshot of the menu | Screenshot of the menu | ||
[[File:pdbe_plugin_menu.png|options|Screenshot of the PyMOL plugin menu with the PDBe plugin installed]] | |||
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[[File:Pdbe_3unb_all_annotation.png|options|All PDBe annotations shown on PDB entry 3unb]] | |||
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This highlights the chemically distinct molecules which make up a PDB entry, including proteins, nucleic acids and ligands. Each molecule is given a unique colour and selected as a different object. Polymers (protein, DNA and RNA chains) are shown as cartoon or ribbon representation and ligands are shown as spheres. | This highlights the chemically distinct molecules which make up a PDB entry, including proteins, nucleic acids and ligands. Each molecule is given a unique colour and selected as a different object. Polymers (protein, DNA and RNA chains) are shown as cartoon or ribbon representation and ligands are shown as spheres. | ||
In the below example the | In the below example the distinct molecules in PDB entry 3l2p are shown. | ||
[[File:Pdbe_3l2p_entity.png|options|Distinct molecules in PDB entry 3l2p]] | |||
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The CATH domains in PDB entry 3b43 are highlighted in the figure below. | The CATH domains in PDB entry 3b43 are highlighted in the figure below. | ||
[[File:Pdbe_3b43_domains.png|options|CATH domains shown on PDB entry 3unb]] | |||
=== PDBe Validation Loader === | === PDBe Validation Loader === | ||
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Geometric validation is shown on PDB entry 2gc2 | Geometric validation is shown on PDB entry 2gc2 | ||
[[File:Pdbe_2gc2_validation.png|options|Geometric validation shown on PDB entry 2gc2]] | |||
=== Assembly Loader === | === Assembly Loader === | ||
Revision as of 15:20, 22 June 2016
PDBe PyMOL plugin
PDBe’s PyMOL plugin provides an easy way to visualise PDB data (and annotations?) in PyMOL. This plugin allows easy access to annotation of entities, domains and validation for PDB entries based on PDBe API.
Installation
The PDBe PyMOL plugin works on PyMOL 1.6 or later
PyMOL 1.6
Download the plugin from the following URL:
PyMOL 1.7 or later
Open the “plugin manager” Enter the following url in the “Install from PyMOL Wiki or URL
This will add the following items to the Plugins menu. PDBe Entity Loader PDBe Domain Loader PDBe Validation Loader Assembly Loader
Screenshot of the menu
To use each component click the menu item in the Plugins menu and then enter and PDB ID into the dialogue box.
PDBe Loader
This displays chemically distinct molecules, domains which make up a PDB entry. It also displays the assemblies within a PDB entry.
Chemically distinct molecules which make up a PDB entry, including proteins, nucleic acids and ligands, are highlighted. Each molecule is given a unique colour and selected as a different object. Polymers (protein, DNA and RNA chains) are shown as cartoon or ribbon representation and ligands are shown as spheres. Pfam, SCOP and CATH domains within a PDB entry are highlighted. Each domain is coloured in a different colour and selected as a different object. This enables each domain to be turned on and off with PyMOL. Assemblies annotated within a PDB entry are highlighted. This requires pymol 1.76 or later.
All PDBe annotations show in PDB entry 3unb
PDBe Molecule Loader
This highlights the chemically distinct molecules which make up a PDB entry, including proteins, nucleic acids and ligands. Each molecule is given a unique colour and selected as a different object. Polymers (protein, DNA and RNA chains) are shown as cartoon or ribbon representation and ligands are shown as spheres.
In the below example the distinct molecules in PDB entry 3l2p are shown.
PDB Domain Loader
This highlights the Pfam, SCOP and CATH domains within a PDB entry. Each domain is coloured in a different colour and selected as a different object. This enables each domain to be turned on and off with PyMOL.
The CATH domains in PDB entry 3b43 are highlighted in the figure below.
PDBe Validation Loader
This overlays geometric validation on a PDB entry. Geometry outliers are coloured as per the PDB validation report: Residues with no geometric outliers are shown in green Residues with one geometric outliers are shown in yellow Residues with two geometric outliers are shown in orange Residues with three or more geometric outliers are shown in red.
Geometric validation is shown on PDB entry 2gc2
Assembly Loader
This highlights the assemblies within a PDB entry. This requires pymol 1.76 or later.
Assemblies are shown within PDB entry 3unb, with each assembly as an object in pymol and coloured in a distinct colour.