[phenixbb] phosphate stereochemistry
rwgrosse-kunstleve at lbl.gov
Sat Jan 14 15:31:06 PST 2012
Did you look in the .geo file?
It should show you all NCS pair distances. Very large differences between
NCS copies will be flagged as "excessive".
On Sat, Jan 14, 2012 at 10:51 AM, Luca Pellegrini <lp212 at cam.ac.uk> 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.
> 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?
>> On 1/6/12 4:31 AM, Luca Pellegrini wrote:
>>> 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,
>>> 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).
>>> 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
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> 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
> phenixbb mailing list
> phenixbb at phenix-online.org
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