[phenixbb] Using phenix.pdbtools to strip multiple conformations out of a PDB file?

Pavel Afonine PAfonine at lbl.gov
Tue Aug 4 08:23:09 PDT 2009

Hi Stephen,

you cannot select on values of occupancies or B-factors, but you can do 
for examples this (which is not exactly what you asked):

- remove all atoms with non-blanc altLoc identifiers:

phenix.pdbtools pdb1akg.ent keep=\"altloc\ '\ '\"

- keep everything except altLoc B:

phenix.pdbtools pdb1akg.ent remove="altloc B"


On 8/4/09 2:26 AM, Stephen Graham wrote:
> Dear all,
> Apologies if this is a dumb question, but I couldn't find the answer
> in the docs or by asking the googlebrain.  Is there a simple way in
> phenix.pdbtools to strip "alternate conformations" of side chains,
> etc, from an input PDB file?  By removing "alternate conformations" I
> mean I would like to keep the conformation with the highest occupancy
> (not necessarily denoted 'A' in the altLoc column) unless all
> conformations have an equal occupancy, in which case I'd arbitrarily
> keep conformation 'A'.
> I think it should be possible by a clever atom_selection command, but
> the correct syntax has thus-far eluded me!
> Thanks,
> Stephen

More information about the phenixbb mailing list