I'm having a bit of an issue with phenix.refine. I was receiving the following error "number of groups of duplicate atom labels: 4789 total number of affected atoms: 9578" However when I looked inside my .pdb file there where only 4789 atoms total....No duplicates. I discovered that phenix.refine is auto selecting a .pdb from a previous run. I found this out by not selecting any .pdb file and found phenix.refine refining my data with an older model I use to refine a previous round. How can I stop phenix.refine from auto selecting a .pdb during refinement? __________________________________ From: [email protected] [[email protected]] on behalf of Pavel Afonine [[email protected]] Sent: Friday, January 20, 2012 12:20 PM To: PHENIX user mailing list Subject: Re: [phenixbb] phosphate stereochemistry 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:

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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:

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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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