phenix.refine and multi-metals centers
Hi I have a doubt on the refinement of e doubled metal center. I know that: 1) one may fix the metals to their actual positions by using e.g. refine.sites.individual="not element Fe" 2) one may use "phenix.metal_coordination my.pdb" to obtain a dictionary for the actual metals coordinations but how does phenix.refine handels metal-to-metal interactions? How should one set the refinement of a metallo protein with a two metals centre, in order not to bias the final result (metal to metal distances) ? Thanks a lot, Carlos -- ************************************** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, Portugal Phone: (351)-214469666 FAX: (351)-214433644 e-mail: [email protected] www.itqb.unl.pt
but how does phenix.refine handels metal-to-metal interactions? How should one set the refinement of a metallo protein with a two metals centre, in order not to bias the final result (metal to metal distances) ?
Roughly, there are two possible approaches: - manually create a .cif file, maybe based on the one you got from phenix.metal_coordination - follow the examples in the "Definition of custom bonds and angles" section of the phenix.refine documentation (https://www.phenix-online.org/documentation/refinement.htm) Without understanding your situation very well, I recommend you try the simple custom bonds and angles first, while keeping the .cif file you got from phenix.metal_coordination . If this doesn't work out, please email me the relevant fragments from your pdb file (metals plus neighboring residues) and I'll take a closer look. Ralf
participants (2)
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Carlos Frazao
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Ralf W. Grosse-Kunstleve