[phenixbb] Problem with Molprobity analysis in phenix 1.6.4

Pavel Afonine pafonine at lbl.gov
Wed Oct 6 07:37:44 PDT 2010

  Hi Florian,

a paper is coming in next Acta D that will be discussing it to some 
(more or less deep) extent:

      Joint X-ray and neutron refinement with /phenix.refine/

      P. V. Afonine, M. Mustyakimov, R. W. Grosse-Kunstleve, N. W.
      Moriarty, P. Langan and P. D. Adams

I hope it will be out in few weeks.

In addition you can have a look:

Acta Cryst. (2010). D66, 12-21
MolProbity: all-atom structure validation for macromolecular crystallography
V. B. Chen, W. B. Arendall III, J. J. Headd, D. A. Keedy, R. M. 
Immormino, G. J. Kapral, L. W. Murray, J. S. Richardson and D. C. Richardson


J. Appl. Cryst. (2010). 43, 669-676
phenix.model_vs_data: a high-level tool for the calculation of 
crystallographic model and data statistics
P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W. 
Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart 
and P. D. Adams

(especially focusing on section 3.1.5).

Probably we need a specific discussion and investigation on what's 
happening at that low (4A) resolution. I've never systematically looked 
into it. So you are hitting a bit of a gray area now.


On 10/6/10 6:56 AM, Florian Schmitzberger wrote:
> Dear Mark,
> I would be quite interested in opinions about the usage and assignment 
> of hydrogens in the riding position for refinement too, especially at 
> low resolution of  around 4 A. How important are they for obtaining 
> reasonable geometry at that resolution?
> From what I could see in the phenix manual hydrogens should should not 
> be included into NCS or TLS groups and are automatically excluded from 
> them.
> Cheers,
> Florian

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