[phenixbb] how to cut off side chain from a model

Pavel Afonine pafonine at lbl.gov
Mon Feb 14 09:06:04 PST 2011


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 

- 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:


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