[phenixbb] running geometry regularization on side chains only
pafonine at lbl.gov
Tue Jul 26 23:10:32 PDT 2011
> Is it possible to do
> phenix.pdbtools model.pdb --geometry_regularization
> but only allow sidechains to be corrected during the process?
no, sorry. This is something that I have no good excuse for, but I
simply need to spend a day to make it clean: let atom selections,
external restraints and CIF files, etc.
Right now there is a dirty way of doing this using phenix.refine:
step 1: create a dummy data file:
phenix.fmodel model.pdb high_res=5 type=real r_free=0.1 label=f-obs
step 2: run phenix.refine:
phenix.refine model.pdb data.mtz strategy=individual_sites
"strategy=individual_sites": requests to refine coordinates only;
"main.bulk_sol=false": turns off bulk-solvent correction and scaling;
"main.number_of_macro_cycles=20": asks for "many" macro-cycles to
"refine.sites.individual=sidechain": asks to refine side chain atoms only;
"wxc_scale=0": turns off X-ray term, since refinement target is T = wxc
* wxc_scale * Txray + wc * Trestraints, and wc=1 by default.
Note, atoms selection syntax used in "refine.sites.individual=sidechain"
is very flexible , you can be very specific about selected atoms. The
are examples in docs.
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