[phenixbb] How to apply geometry regularization to selected residues in phenix.pdbtools

[Pavel Afonine]

Hi Oliv,

phenix.pdbtools my.pdb  --geometry-regularization

applies to the whole structure. It's an overlook on my end - till today 
I believed it uses atom selections. I will fix it.

For the moment you can you phenix.refine for this:

phenix.refine model.pdb data.mtz strategy=individual_sites 
main.bulk_solvent=false wxc_scale=0 refine.sites.individual="chain A and 
resseq 123"

By using wxc_scale=0 you ask phenix.refine to ignore experimental data 
(although you still have to give a data file, but in this case you can 
use a fake one).

Pavel.
 

On 6/22/09 7:08 PM, Oliv Eidam wrote:
> Hi,
>
> I was wondering if the geometry regularization in phenix.pdbtools can 
> be applied to selected residues only.
> Something like:
> > phenix.pdbtools my.pdb  selection="resname xyz" 
> --geometry-regularization
>
> Many thanks in advance,
>
>   Oliv
>
>
> -- 
> Oliv Eidam, Ph.D.
> Postdoctoral fellow
>
> University of California, San Francisco
> Dept. of Pharmaceutical Chemistry
> 1700 4th Street, Byers Hall North, Room 501
> San Francisco, CA 94158 - Box 2550
>
> Phone: 415-514-4253
> Fax  : 415-514-4260
> Email: eidamo at blur.compbio.ucsf.edu <mailto:eidamo at blur.compbio.ucsf.edu>
> ------------------------------------------------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090624/a3085da1/attachment-0003.htm>