Re: [ccp4bb] Archiving Images for PDB Depositions

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Subject: Re: Archiving Images for PDB Depositions
From: Felix Frolow mbfrolow {- at -} POST {- dot -} TAU {- dot -} AC {- dot -} IL
Date: 2011-11-03

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Subject: Re: Archiving Images for PDB Depositions
From: Felix Frolow mbfrolow {- at -} POST {- dot -} TAU {- dot -} AC {- dot -} IL
Date: 2011-11-03

Clemens,
In the past, we have used TRACER (free domain) for higher symmetry or we interpreted manually Niggly values :-)
TRACER is gone long time ago. Niggly values are not displayed anymore, so we trust auto indexing of DENZO which, assuming all experimental parameters are properly set ( we do this by using a standard crystal such as lysozyme) is extremely sensitive in defining Bravais system. I have no experience with POINTLESS, but assume that it is also doing an excellent work.

FF

Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfrolow@post.tau.ac.il
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On Nov 3, 2011, at 22:27 , Clemens Vonrhein wrote:

> On Thu, Nov 03, 2011 at 04:13:44PM -0400, Bryan Lepore wrote:
>> not sure I follow this thread, but this table might be interesting :
>>
>> http://journals.iucr.org/d/issues/2010/05/00/dz5193/dz5193sup1.pdf
>>
>> from:
>>
>> Detection and correction of underassigned rotational symmetry prior to
>> structure deposition
>> B. K. Poon, R. W. Grosse-Kunstleve, P. H. Zwart and N. K. Sauter
>> Acta Cryst. (2010). D66, 503-513 [ doi:10.1107/S0907444910001502 ]
>
> Oh yes, that is relevant and very interesting. As far as I understand
> it, the detection of higher symmetry is based on the atomic
> coordinates and not structure factors though (please correct me if I'm
> wrong here).
>
> At least some of the cases for which the deposited structure factors
> strongly suggest a higher symmetry don't seem to be detected using
> that papers approach (I can't find them listed in the supplemental).
>
> Cheers
>
> Clemens
>
> --
>
> ***************************************************************
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> *
> * Global Phasing Ltd.
> * Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK
> *--------------------------------------------------------------
> * BUSTER Development Group (http://www.globalphasing.com)
> ***************************************************************

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Archiving Images for PDB Depositions
From: Felix Frolow mbfrolow {- at -} POST {- dot -} TAU {- dot -} AC {- dot -} IL
Date: 2011-11-03

Next message:
Subject: Re: off-topic: Topology diagram
From: Petr Leiman petr {- dot -} leiman {- at -} EPFL {- dot -} CH
Date: 2011-11-03