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

Edward A. Berry BerryE at upstate.edu
Mon Feb 14 09:53:25 PST 2011

This seems very flexible and general indeed, but for the specific
job of making an MR model, it could be very tedious to code which
atoms to keep for which residues, where to delete, and how to renumber.
Chainsaw does all of that for you.
With the "keep atoms in common", it deletes all atoms that don't exist
in the target structure- for example if the real protein has a glycine,
it doesn't make much sense to trim the model to alanine. On the other
hand if the protein has asp and the model glu, you might want to keep
Cg as well.
And based on the alignment you give it, which is the only input other
than the model pdb, it will decide where to delete residues and renumber
to the target sequence taking into account gaps and inserts. Which you
can control by editing the alignment.

Pavel Afonine wrote:
> 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.
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list