[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
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----- 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
> -------------------------------
>
>
>
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> Forschungszentrum Juelich GmbH
> 52425 Juelich
>
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> Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,
> Dr. Sebastian M. Schmidt
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-------------------------------------------------------------------
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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
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