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@blur.compbio.ucsf.edu
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