PDBFixer is changing chain names

[raoufkeskes]

hello,

PDBfixer in my case is changing chain names and re-indexing them to alphabet order

initial chains are : {'O', 'F', 'D', 'P'}
fixed PDB chains are : {'A', 'B', 'C', 'D'}

fixer = PDBFixer(filename="my_structure.pdb")
fixer.findMissingResidues()
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
PDBFile.writeFile(fixer.topology, fixer.positions, open("my_fixed_structure.pdb", 'w'))

my structure : https://www.filemail.com/d/rrqrxvfuhrgxkdp

[peastman]

In the call to writeFile(), add the argument keepIds=True. See the API documentation at http://docs.openmm.org/latest/api-python/generated/openmm.app.pdbfile.PDBFile.html#openmm.app.pdbfile.PDBFile.writeFile, especially the warning about that argument.