[phenixbb] phosphate stereochemistry

[Dale Tronrud]

   I don't know if this is the case for Phenix, but some programs apply restraints
that keep the phosphate tetrahedral.  If the names of the two oxygen atoms that
stick out are swapped relative to these restraints all sorts of mischief occurs.
Try swapping the names and see if that makes the problem go away.

Dale Tronrud

On 01/06/12 04:31, Luca Pellegrini wrote:
> Hi,
> 
> I have noticed that Phenix mangles O-P bond lengths and angles in the phosphate groups of my DNA chain (example in pict attached). This only happens to 3 out of 28 phosphates. The refined protein-DNA structure does not present any other unusual stereochemistry issues and refinement runs normally. Could anybody advice on what is going on and how to fix this, please?
> 
> I am using Phenix-1.7.3-928. Refinement is with default target weights, hydrogens on and does not include simulated annealing. I could make the stereochemistry targets more stringent, but the default values seem strict enough (bond and angle rmsd is 0.005 and 1.225).
> 
> Thanks,
> Luca  
> 
> Luca Pellegrini
> Department of Biochemistry
> University of Cambridge
> 80 Tennis Court Road
> Cambridge CB2 1GA - UK
> 
> Email: lp212 at cam.ac.uk
> Tel: 0044-1223-760469
> Fax: 0044-1223-766002
> Sanger building, room 3.59
> 
> 
> 
> 
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