[phenixbb] phosphate stereochemistry

Luca Pellegrini lp212 at cam.ac.uk
Fri Jan 20 10:53:23 PST 2012

Hi Pavel,

NCS was set to 'global' in the refinement gui. Setting it to 'torsion' does seem to maintain the correct geometry.


On 20 Jan 2012, at 17:20, Pavel Afonine wrote:

> Hi Luca,
> what kind of NCS restraints did you use: torsion or Cartesian? I wonder if torsion NCS would naturally avoid this problem? I hope Jeff comments on this.
> Pavel
> On 1/14/12 10:51 AM, Luca Pellegrini wrote:
>> I think I discovered what was happening to my DNA molecule during refinement, that caused distortion of the phosphate groups. It was something along the lines of what Dale suggested, I mention it here so that it might be useful to others.
>> I have two DNA molecules in the ASU and I didn't realised that I had accidentally swapped OP1 and OP2 in 3 out of 28 phosphates (so that, if the two DNA molecules were superimposed, OP1 ended on top of OP2). Because I had NCS restraints on during refinement, I guess phenix was trying to move OP1 in one DNA molecule towards the NCS-equivalent position of OP1 in the second molecule, hence the altered geometry.
>> I have fixed the atom nomenclature problem and now the geometry of my DNA is ok. I appreciate that most people tend to avoid such mistakes ;-) but perhaps it would be good if phenix could flag situations such as these.
>> Luca
>> On 6 Jan 2012, at 16:15, Pavel Afonine wrote:
>>> 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
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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
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