[phenixbb] DNA double helix with many molprobity bad clashes

Morten Groftehauge mortengroftehauge.work at gmail.com
Fri Nov 30 03:14:35 PST 2012

Hi Christian,

Check that your OP1 and OP2 aren't swapped. Phenix doesn't check for this
and is unable to resolve it automatically but your geometry gets distorted
if they are swapped.

Get back to us if you resolve the problem.


On 21 November 2012 17:17, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Benda,
>  I am refining a protein-DNA complex at around 3 A with a standard b-form
>> dsDNA. R-factors are around 24/20 (kinda low for the resolution).
>> Originally, I placed the DNA using coot and now, after several rounds of
>> refinement in phenix, I get a long list of bad clashes from molprobity
>> validation (in phenix) that covers the whole length of the DNA and almost
>> exclusively lists hydrogens from the ribose moiety (whether or not in
>> contact with protein). My question is,
>> - why is phenix.refine not taking care of these clashes (i.e. optimizes
>> the structure such that they go away)?. Am I giving experimental
>> contribution to high a weight  (I have  "optimize x-ray/stereochemistry"
>> checked)?
> because if the model is in a local minimum minimization will not kick it
> out of it. Simulated annealing refinement (available in phenix.refine) is
> the tool for this.
> This is illustrated on pages 67-71 here:
> http://www.phenix-online.org/**presentations/latest/pavel_**
> refinement_general.pdf<http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf>
> Simply make sure you are using recent Phenix version (so you get
> consistent clash-scores with Molprobity), add H atoms and run SA refinement.
> Pavel
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Morten K Grøftehauge, PhD
Pohl Group
Durham University
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