[ccp4bb] translation of atom sites and maps

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

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Subject: Ph.D. student and Postdoctoral positions in Structural Biology/Biophysics at the Swiss Federal Institute of Technology in Lausanne (EPFL)
From: Petr Leiman leiman {- at -} PURDUE {- dot -} EDU
Date: 2008-08-05

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Subject: Re: translation of atom sites and maps
From: Graeme Winter graeme {- dot -} winter {- at -} GOOGLEMAIL {- dot -} COM
Date: 2008-08-06

Subject: translation of atom sites and maps
From: David Waterman waterman {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-08-06

Hi,

I have a SAD dataset in F23 that I have solved using both SHELX (via
hkl2map) and phenix, and for my own obscure reasons I want to compare the
results. Both SHELXD and phenix.hyss find 2 sites and both pipelines go on
to produce protein-like maps. I opened the heavy atom sites in Coot and was
surprised to find that the two sets of sites were different - that is, they
were not related by crystallographic symmetry. However, after looking a
little deeper, I found the tool phenix.emma, which told me that the sites
were indeed related, by a translation of {0.25, 0.25, 0.25}.

I must admit I'm confused about how this can be the case (I thought there
was only one choice of origin?), but I'd still like to compare the results.
I can easily edit one of the pdb files of the heavy atom sites to cause the
required translation, however in order to translate the maps for comparison
in Coot I need to do something more complicated, like rotate all of the
phases in one of the MTZ files by a various amounts. How can I change an MTZ
file to result in a real space translation of the electron density?

Cheers
David

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

Next message:
Subject: Re: translation of atom sites and maps
From: Graeme Winter graeme {- dot -} winter {- at -} GOOGLEMAIL {- dot -} COM
Date: 2008-08-06