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

Stephen Graham stepheng at strubi.ox.ac.uk
Tue Aug 4 02:26:59 PDT 2009

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!



Dr Stephen Graham
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549

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