[phenixbb] metal coordination

Nigel Moriarty nwmoriarty at lbl.gov
Mon Apr 30 08:55:25 PDT 2012


phenix.metal_coordination generates a file to add to the phenix.refine
inputs. phenix.refine doesn't use LINK records either reading them in
or writing them out. You can use phenix.link_edits to read the LINK
records in a PDB file and generate an edits file for phenix.refine.

Regarding use of the output from phenix.metal_coordination, you should
use remove the angle restraints or use the phil parameter
output_angles=False during the initial stages of refinement.



On Mon, Apr 30, 2012 at 7:23 AM, Panne Daniel <panne at embl.fr> wrote:
> Hi all,
> I had a question concerning metal coordination (zinc in this case). I have
> used phenix.metal_coordination to generate geometry restraints for
> refinement. However phenix.refine does not write out the necessary LINK
> records into the PDB file. This seems to lead to problems later during
> validation, as the metal coordination is not properly recognized. What would
> be the best way to generate the LINK records in Phenix?
> Thanks,
> Daniel
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

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