[phenixbb] running geometry regularization on side chains only

Pavel Afonine pafonine at lbl.gov
Tue Jul 26 23:10:32 PDT 2011

Hi Francois,

> 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 
main.bulk_sol=false main.number_of_macro_cycles=20 
refine.sites.individual=sidechain wxc_scale=0

"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 
achieve convergence;
"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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