[phenixbb] metal coordination restraints

Pavel Afonine pafonine at lbl.gov
Fri Nov 4 09:44:44 PDT 2011

Hi Laurie,

> How does PHENIX know where to look for proper bond lengths and angles 
> for a metal ion I add to a protein structure - do I just add the metal 
> into difference density and any waters, and then run ready set and it 
> knows where to look for that particular metal and the atoms to which 
> is is coordinated?  And shouldn't there be a 'cif file that it 
> outputs, or is that something that I need to get myself?  Sorry it's 
> still not obvious to me from the documentation.

step 1: you run

phenix.metal_coordination model.pdb

it will create .edits file containing necessary restraints.

step 2: have a look at this file to make sure the restraints match your 

step 3: use .edits file in refinement.

Let me know if you have any more questions or need help with this.


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