On 07/27/2011 03:10 PM, Pavel Afonine wrote:
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:
Thanks for the workaround Pavel. However, I just wanted to know if it could be done using geometry only with phenix.pdbtools. If it was possible and fast, I or some colleague may have needed to wrap the functionality into some code as a compiled library. Maybe I should rather look for some tool that can add sidechains to a backbone model (without introducing clashes in the process). Thanks a lot, Francois.
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.
Pavel.
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