search

openmm / pdbfixer

PDBFixer fixes problems in PDB files
Other
443 stars 112 forks source link

Select residue atom positions for residues with alternate locations (altloc) #253

Closed JSLJ23 closed 1 year ago

JSLJ23 commented 1 year ago

Hi developers of PDBfixer,

I was wondering, how do I select which one of the alternate locations (altloc) of a residue to retain in the fixed PDB? For example in 3HYD (https://www.rcsb.org/structure/3HYD), GLU 3 has two possible positions A & B but PDB fixer by default only saves position A. On the README, it is mentioned that PDBfixer can:

However I am unable to find any information in the docs which might suggest how this could be done. I am hoping to get some help here so raising this as an issue.

peastman commented 1 year ago

There's no option to select that. It just uses the first one. Do you have an application where it's important to specify a particular one?

noahharrison64 commented 1 year ago

An application where this might be useful would be multitemperature PDBs

JSLJ23 commented 1 year ago

When PDB fixer selects these residue altlocs, does it do so based on highest occupancy or just the first occurrence?

peastman commented 1 year ago

It uses the first one in the file.