Difference between revisions of "PDB plugin"

From PyMOLWiki
Jump to: navigation, search
(updated image)
 
(12 intermediate revisions by 2 users not shown)
Line 1: Line 1:
== PDBe PyMOL plugin ==
+
== PDB 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.
+
PDBe’s PyMOL plugin provides an easy way to visualise PDB data and annotations in PyMOL. This includes displaying individual molecules, Pfam, SCOP and CATH domains and viewing geometric validation for PDB entries based on PDBe's API.
 
   
 
   
 
=== Installation ===
 
=== Installation ===
 
   
 
   
The PDBe PyMOL plugin works on PyMOL 1.6 or later
+
The PDB PyMOL plugin works on PyMOL 1.6 or later
 
   
 
   
 
==== PyMOL 1.6 ====
 
==== PyMOL 1.6 ====
 
Download the plugin from the following URL:
 
Download the plugin from the following URL:
  
 +
http://www.ebi.ac.uk/pdbe/pdb-component-library/pymol_plugin/PDB_plugin.py
  
 
 
==== PyMOL 1.7 or later ====
 
==== PyMOL 1.7 or later ====
 
Open the “plugin manager”
 
Open the “plugin manager”
 
Enter the following url in the “Install from PyMOL Wiki or URL
 
Enter the following url in the “Install from PyMOL Wiki or URL
 +
 +
http://www.ebi.ac.uk/pdbe/pdb-component-library/pymol_plugin/PDB_plugin.py
 
   
 
   
This will add the following items to the Plugins menu.
+
This will add the following items to the Plugins menu:
PDBe Entity Loader
+
 
PDBe Domain Loader
+
PDB Analysis - All
PDBe Validation Loader
+
 
Assembly Loader
+
PDB Analysis - Molecules
 +
 
 +
PDB Analysis - Domains
 +
 
 +
PDB Analysis - Validation
 +
 
 +
PDB Analysis - Assemblies
 +
 
  
 
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]]
+
[[File:PDB_plugin.png|options|Screenshot of the PyMOL plugin menu with the PDB plugin installed]]
  
 
   
 
   
 
To use each component click the menu item in the Plugins menu and then enter and PDB ID into the dialogue box.
 
To use each component click the menu item in the Plugins menu and then enter and PDB ID into the dialogue box.
  
=== PDBe Loader ===
+
=== PDB Analysis - All ===
  
 
This displays chemically distinct molecules, domains which make up a PDB entry. It also displays the assemblies within a PDB entry.  
 
This displays chemically distinct molecules, domains which make up a PDB entry. It also displays the assemblies within a PDB entry.  
Line 38: Line 47:
 
Assemblies annotated within a PDB entry are highlighted. This requires pymol 1.76 or later.  
 
Assemblies annotated within a PDB entry are highlighted. This requires pymol 1.76 or later.  
  
All PDBe annotations show in PDB entry 3unb
+
All PDB annotations show in PDB entry 3unb
  
  
[[File:Pdbe_3unb_all_annotation.png|options|All PDBe annotations shown on PDB entry 3unb]]
+
[[File:Pdbe_3unb_all_annotation.png|800x800px|All PDB annotations shown on PDB entry 3unb]]
  
 
   
 
   
=== PDBe Molecule Loader ===
+
=== PDB Analysis - Molecules ===
 
   
 
   
 
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.   
Line 51: Line 60:
  
  
[[File:Pdbe_3l2p_entity.png|options|Distinct molecules in PDB entry 3l2p]]
+
[[File:Pdbe_3l2p_entity.png|800x800px|Distinct molecules in PDB entry 3l2p]]
  
 
   
 
   
=== PDB Domain Loader ===
+
=== PDB Analysis - Domains ===
 
   
 
   
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.
+
This highlights the Pfam, Rfam, 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 Domains Plugin also highlights chemically distinct molecules and domains are overlaid on these molecules.
 
   
 
   
 
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]]
+
[[File:PDBe_3b43_domains_2.png|800x800px|CATH domains shown on PDB entry 3b43]]
  
=== PDBe Validation Loader ===
+
=== PDB Analysis - Validation ===
 
   
 
   
 
This overlays geometric validation on a PDB entry. Geometry outliers are coloured as per the PDB validation report:
 
This overlays geometric validation on a PDB entry. Geometry outliers are coloured as per the PDB validation report:
Line 74: Line 83:
  
  
[[File:Pdbe_2gc2_validation.png|options|Geometric validation shown on PDB entry 2gc2]]
+
[[File:Pdbe_2gc2_validation.png|800x800px|Geometric validation shown on PDB entry 2gc2]]
  
=== Assembly Loader ===
+
=== PDB Analysis - Assemblies ===
  
 
This highlights the assemblies within a PDB entry. This requires pymol 1.76 or later.
 
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.
+
Assemblies are shown within PDB entry 5j96, with each assembly as an object in pymol and coloured in a distinct colour.
 +
 
 +
 
 +
[[File:PDB_5j96_assemblies.png|800x800px|Assemblies shown for PDB entry 5j96]]
 +
 
 +
 
 +
=== View assemblies for your own mmCIF file ===
 +
 
 +
To view annotated assemblies in your own mmCIF file - for example after PDB annotation - run pymol with the following command:
 +
 
 +
pymol -r PDB_plugin.py -- mmCIF_file=YOUR_MMCIF_FILE
 +
 
 +
where YOUR_MMCIF_FILE is the filename you want display the assemblies for.
 +
 
 +
 
 +
=== Acknowledgements ===
 +
 
 +
This plugin was developed by PDBe
 +
[[File:Pdbe_logo.png|100x100px|link=http://pdbe.org|PDBe logo]]
 +
who are a founding member of the wwPDB
 +
[[File:Wwpdb-logo.png|200x200px|link=http://www.wwpdb.org/|wwPDB logo]]
 +
 
 +
 
 +
 
 +
 
 +
[[Category:Plugins]]
 +
[[Category:Structural_Biology_Scripts]]

Latest revision as of 14:09, 12 June 2018

PDB PyMOL plugin

PDBe’s PyMOL plugin provides an easy way to visualise PDB data and annotations in PyMOL. This includes displaying individual molecules, Pfam, SCOP and CATH domains and viewing geometric validation for PDB entries based on PDBe's API.

Installation

The PDB PyMOL plugin works on PyMOL 1.6 or later

PyMOL 1.6

Download the plugin from the following URL:

http://www.ebi.ac.uk/pdbe/pdb-component-library/pymol_plugin/PDB_plugin.py

PyMOL 1.7 or later

Open the “plugin manager” Enter the following url in the “Install from PyMOL Wiki or URL

http://www.ebi.ac.uk/pdbe/pdb-component-library/pymol_plugin/PDB_plugin.py

This will add the following items to the Plugins menu:

PDB Analysis - All

PDB Analysis - Molecules

PDB Analysis - Domains

PDB Analysis - Validation

PDB Analysis - Assemblies


Screenshot of the menu


Screenshot of the PyMOL plugin menu with the PDB plugin installed


To use each component click the menu item in the Plugins menu and then enter and PDB ID into the dialogue box.

PDB Analysis - All

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 PDB annotations show in PDB entry 3unb


All PDB annotations shown on PDB entry 3unb


PDB Analysis - Molecules

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.


Distinct molecules in PDB entry 3l2p


PDB Analysis - Domains

This highlights the Pfam, Rfam, 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 Domains Plugin also highlights chemically distinct molecules and domains are overlaid on these molecules.

The CATH domains in PDB entry 3b43 are highlighted in the figure below.


CATH domains shown on PDB entry 3b43

PDB Analysis - Validation

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


Geometric validation shown on PDB entry 2gc2

PDB Analysis - Assemblies

This highlights the assemblies within a PDB entry. This requires pymol 1.76 or later.

Assemblies are shown within PDB entry 5j96, with each assembly as an object in pymol and coloured in a distinct colour.


Assemblies shown for PDB entry 5j96


View assemblies for your own mmCIF file

To view annotated assemblies in your own mmCIF file - for example after PDB annotation - run pymol with the following command:

pymol -r PDB_plugin.py -- mmCIF_file=YOUR_MMCIF_FILE

where YOUR_MMCIF_FILE is the filename you want display the assemblies for.


Acknowledgements

This plugin was developed by PDBe PDBe logo who are a founding member of the wwPDB wwPDB logo