[phenixbb] phenix.refine is auto selecting an old .pdb file for refinement

Andrews, Forest Hoyt foandrew at imail.iu.edu
Fri Jan 20 10:39:39 PST 2012

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: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Pavel Afonine [pafonine at lbl.gov]
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.


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

phenixbb mailing list
phenixbb at phenix-online.org

More information about the phenixbb mailing list