Re: [ccp4bb] translation of atom sites and maps

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

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Subject: Re: translation of atom sites and maps
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2008-08-06

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

Dear all,

Thanks for the responses. 'Phase comparison' (phasematch) produced nicely
aligned maps after changing the origin of one set of SFs, and it looks like
it will give some nice statistics for more quantitative comparison, which is
what I want to do eventually...

The confusion came from my limited interpretation of Int. Tab. A. There are
more options for the origin than I appreciated.

Cheers
David

phasematch is in the GUI
E

Graeme Winter wrote:

Hi David,

There is a clipper utility called "cphasematch" which will do exactly
this. More info here:

http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html

or you can get the updates against ccp4 6.0.2 through the ccp4 downloads
pages.

Cheers,

Graeme

2008/8/6 David Waterman :

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

CCP4bb navigation

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

Previous message:
Subject: Re: translation of atom sites and maps
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2008-08-06