[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
}
}
Engin
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