[phenixbb] special positions

o.h.weiergraeber at fz-juelich.de o.h.weiergraeber at fz-juelich.de
Wed Jul 2 08:41:38 PDT 2008


Adding to my previous post, I have found another strange issue (possibly a bug?) concerning special positions:
In my case, the "special" atom (a cation on a three-fold in sg I23), while being considered during refinement, seems to be completely omitted (or heavily downweighted) for map calculations! The 2fo-fc map shows a "hole" at this position, while there is huge difference density in the fo-fc map (largely irrespective of whether or not the occupancy is reduced in the input.)
The same pdb file, used in cns just for map calculation, gives a beautiful density at the cation position, while the rest of the map is more or less identical.

At the moment I cannot think of any error in the input since refinement of the atom does take place, with the proper restrictions due to the three-fold axis.
But something is going seriously wrong.

Any ideas?
Oliver



-------------------------------
 Dr. Oliver H. Weiergraeber
 Institute of Neurosciences and Biophysics
 Molecular Biophysics
 Research Centre Juelich
 D-52425 Juelich
 Germany
 Phone: +49-2461-612028
 Fax: +49-2461-612020
-------------------------------

----- Original Message -----
From: o.h.weiergraeber at fz-juelich.de
Date: Wednesday, July 2, 2008 2:55 pm
Subject: [phenixbb] special positions

> Hello,
> 
> a very simple question (although I could not find *anything* about 
> this in the documentation!):
> What does phenix.refine expect as occupancy for an atom on a 
> special position: reduced occupancy (like refmac) or full occupancy 
> (like cns_solve)?
> 
> Oliver
> 
> 
> 
> -------------------------------
> Dr. Oliver H. Weiergraeber
> Institute of Neurosciences and Biophysics
> Molecular Biophysics
> Research Centre Juelich
> D-52425 Juelich
> Germany
> Phone: +49-2461-612028
> Fax: +49-2461-612020
> -------------------------------
> 
> 
> 
> -------------------------------------------------------------------
> -------------------------------------------------------------------
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> 
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe
> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,
> Dr. Sebastian M. Schmidt
> -------------------------------------------------------------------
> -------------------------------------------------------------------
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
> 



-------------------------------------------------------------------
-------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich

Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,
Dr. Sebastian M. Schmidt
-------------------------------------------------------------------
-------------------------------------------------------------------



More information about the phenixbb mailing list