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FAQ & Troubleshootings  

Could not find all the chains expected in pdb XXXX.

>> So far, InterEvol processed and clustered only protein-protein complexes but not peptide-protein complexes.
Chains with less than 30 amino acids were not considered in the clustering step and were discarded
For example, in PDB 1a09, the peptide ligand was not considered...

Chain names do not match with those in the original PDB file.

>> To generate the InterEvol database, PDB files were processed to build the assemblies as specified in the paper. When required, chains had to be renamed.
Renaming was also required for pdb files with a large number of chains. The original chain name used to generate InterEvol chain name
is displayed in the chain or interface information panels available in the InterEvol browser.

Residues indexes in the 3D coordinates file downloaded from InterEvol
differ from the indexes in the original PDB file.

>> To facilitate subsequent mapping between the structures and their multiple sequence alignments, chains were renumbered if required
so that the first residue index of every chain is 1 and every subsequent residue index is incremented by 1 (no gaps in the indexes).
In that way, several residues in the 3D structures can be selected in the Pymol Plugin and their corresponding alignment columns displayed.

PDB file XXXX could not be found in the database.

>> InterEvol only collects protein-protein assemblies and not monomeric structures even if homologs of the monomer exist in complex in other PDB structures.
For example, PDB 1blj correspond to a SH2 domain but solved in a monomeric form...

When downloading the PDB file from InterEvol, only ONE chain was found and not TWO as expected for an interface.

>> Beware clicking on the link between two chains to access the interface panel. If only one chain was retrieved, you probably rather clicked on a chain.