Daniel 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. Cheers Nigel On Mon, Apr 30, 2012 at 7:23 AM, Panne Daniel 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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