[phenixbb] phenix.refine and multi-metals centers

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Tue Mar 9 10:46:31 PST 2010

> 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

- follow the examples in the "Definition of custom bonds and angles"
  section of the phenix.refine documentation

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.


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