[phenixbb] special positions

[Folmer Fredslund]

2008/7/2  <o.h.weiergraeber at fz-juelich.de>:
> 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.
>

Hi Oliver,

I don't have any links to manual or anything of that sort, but I
refined a metal ion on a 2-fold axis and I simply put the atom exactly
on the special position. That seemed to work just fine...

Hope this helps,

Folmer

> 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
>> -------------------------------
>>
>>
>>
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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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