[phenixbb] phosphate stereochemistry

Pavel Afonine pafonine at lbl.gov
Fri Jan 20 09:20:41 PST 2012

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.


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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