[phenixbb] default bondlengths - metal

Engin Ozkan eozkan at stanford.edu
Sat Feb 28 09:44:52 PST 2009

Hi, all,

Recently following the phenixbb, I was made aware of 
phenix.metal_coordination.  So I just gave it a try for a structure of 
mine with sodium in it.  Specifically, I decided to turn the 
use-default-bondlengths option on.  The result was surprising, because 
the output file thinks that sodum to oxygen distances are supposed to be 
1.9 Angstroms.  Work done by Marjorie Harding and others have shown that 
this distance should be about 2.4 (Acta Cryst. D62 (2006), 678-682; for 
a summary of their numbers, 
http://tanna.bch.ed.ac.uk/newtargs_06.html).  I wonder why 
phenix.metal_coordination chose 1.9 A as the default Na-O distance, or 
is the default option a different type of bond distance, I am not sure.

Any clarification from the authors would be appreciated.

Below is part of the output, showing the distance:

refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = name NA   and chain N and resname NA and resseq    1
    atom_selection_2 = name  O   and chain A and resname PHE and resseq   76
    distance_ideal = 1.920420
    sigma = 0.01


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