Specific handling of alternative locations

[koyurion]

Hi, Thanks for your great job on PLIP, which benefits me a lot in my current study.

I wonder how does PLIP handle the alternative location of disorder residues (or disorder atom) in PDB.

I find some hints in codes but do not very clearly understand. Are there some documents or references about this?

################################################ dir: "plip/plip/structure/preparation.py /" Protein

Ligand

[koyurion]

Moreover, in one PDB, there are sometimes two or more chains whose structure is the same but represented by different chain IDs (like "A", "B"...). How does the PLIP handle this? Thanks again!

[fkaiserbio]

Currently all but the first alternative location are discarded, unless you specify --altlocation. Then all atoms will be processed. There is no way to select a specific alternative location at the moment. Chains are processed individually.