Plugin shows structure annotations in PyMOL

Screenshot of PDBe PyMOL plugin
10 October 2016

There’s lots of extra data in a PDB entry that isn’t shown in many viewers, making it difficult to view and analyse. PDBe’s PyMOL plugin helps out with this problem by displaying some of this extra information in PyMOL. You can download it from


The plugin comes in four parts:


  • PDB Analysis- Molecules.  This separates molecules that are chemically unique into separate PyMOL objects.  You can easily select (for example) both alpha chains of haemoglobin together, without having to guess which chain IDs they are. They’re labelled with the molecule name in the Object Control Panel, making it really easy.


  • PDB Analysis- Domains. This part of the plugin highlights the different domains of a protein structure. The Pfam, CATH and SCOP defined domains are loaded as different PyMOL objects.


  • PDB Analysis- Validation. In this plugin, the PDB entry is coloured according to the geometric validation in the wwPDB report. Green shows no geometry outliers in the residue, red indicates 3 or more.


  • PDB Analysis - Assemblies. This presents each assembly annotated in the PDB entry as a separate object. No more turning on symmetry and trying to guess which crystallographic dimer is the one you should be looking at!


  • Finally, because you can’t have too much of a good thing, there’s an ‘All’ option, which does all four of the above at the same time.


The plugin is available to download from the PyMOL Wiki pages, in the Plugins section at