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?

Pavel

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: [email protected]
Tel: 0044-1223-760469
Fax: 0044-1223-766002
Sanger building, room 3.59









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