[phenixbb] running geometry regularization on side chains only

Francois Berenger berenger at riken.jp
Tue Jul 26 23:48:33 PDT 2011

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,

> 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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