[phenixbb] phosphate stereochemistry

[Luca Pellegrini]

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
>>
>> 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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>
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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
Sanger building, room 3.59