[phenixbb] phosphate stereochemistry

Pavel Afonine pafonine at lbl.gov
Fri Jan 6 08:15:37 PST 2012

Hi Luca,

phenix.refine always generates a *.geo file that lists all the geometry 
restraints (bonds, angles, planarities, chiralities, dihedral, 
non-bonded, ncs(if any)) used in refinement for all atoms. For each 
restraint it list current model value, target (library) value, etc.

Can you have a look at *.geo file for O-P bonds in question? May be this 
gives a hint about what's going on?


On 1/6/12 4:31 AM, 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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