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

Oliv Eidam eidamo at blur.compbio.ucsf.edu
Wed Jun 24 19:07:29 PDT 2009


Hi Pavel,

Thanks a lot for pointing at the excellent workaround using phenix.refine.
It worked very well and only selected atoms were regularized.

Best, Oliv



On Wed, Jun 24, 2009 at 8:24 AM, Pavel Afonine <PAfonine at lbl.gov> wrote:

>  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
>
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