Thanks, Nigel. I had actually created the restraints manually with the literature values (and that did match what I saw in density). I was just testing this new tool, because it sure is bound to come handy. It also gave me chance to point out the literature on this matter; this work even suggests sigma values specifically for structure refinement. Engin Nigel W Moriarty wrote:
Engin
Thanks for the posting. You have discovered a hole in the coverage of the default bond lengths data. Thanks for the link. I'm sure it will be incorporated in the near future.
In the meantime, I'm sure you are aware that you can change the value in the "edits" file.
Nigel
On 2/28/09 9:44 AM, Engin Ozkan wrote:
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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