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 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: [email protected]

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