[phenixbb] how to cut off side chain from a model
Pavel Afonine
pafonine at lbl.gov
Mon Feb 14 09:06:04 PST 2011
Hi,
as Jeff pointed out last week, using phenix.pdbtools you can be very
selective in what you keep/remove. Just a few examples:
- remove all waters:
phenix.pdbtools model.pdb remove=water
- remove all waters and DNA/RNA:
phenix.pdbtools model.pdb remove="water or dna or rna"
- remove all protein sidechains:
phenix.pdbtools model.pdb remove="protein and sidechain"
or equivalently:
phenix.pdbtools model.pdb keep="all and not (protein and sidechain)"
- keep only oxygens:
phenix.pdbtools model.pdb keep="element O"
- keep only nitrogens in protein sidechains:
phenix.pdbtools model.pdb keep="protein and sidechain and element N"
- keep only backbone in chain A and in chain C:
phenix.pdbtools model.pdb keep="(chain A and backbone) or (chain C and
backbone)"
- remove residues in chain A from number 3 to 25:
phenix.pdbtools model.pdb remove="chain A and resseq 3:25"
... and so on.
To get more familiar with atom selection syntax you can practice by
running the command
phenix.pdb_atom_selection model.pdb ATOM_SELECTION_STRING
for example:
phenix.pdb_atom_selection model.pdb "chain A and resseq 1:100"
which will output the selected atoms to the screen. Some examples of
atom selection syntax can be found here:
http://phenix-online.org/documentation/refinement.htm#anch88
Pavel.
More information about the phenixbb
mailing list