[ccp4bb] 3D-fititng which is actually 2D-fititng

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

Previous message:
Subject: Re: 3D fitting
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-02-26

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Subject: Re: units of f0, f', f''
From: Bernhard Rupp br {- at -} RUPPWEB {- dot -} ORG
Date: 2010-02-26

Subject: 3D-fititng which is actually 2D-fititng
From: Miri Hirshberg miri {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2010-02-26

Fri., Feb. 26th 2010
EBI

Dear all,

I've already replied privately to several people who replied when I first
posted th question, but did not set the record-clear for
the whole community and I do apologize.

What I have is two or more 3D structures, not protein, similar in
their 3D but equivalent atoms don't have the same atom-name. I thought
that in order to rename equivalent atoms automatically I needed to 3D fit
the two structures first. Adel Golovin of PDBeMOTIF fame
(http://www.ebi.ac.uk/pdbe-site/pdbemotif) has pointed out that for the
automatic atom renaming process all I needed was 2D-fitting via 2D-graph
isomorphism routine which he could provide. Once all structures in a given
set have the same atom names, 3D-fitting is doable using numerous
software/utilities.

Thanks again for the replies, especially to Pavel Afonine (phenix)
with whom I had a lengthy exchange.

CCP4-board is one of the best...

Thanks again
Miri

CCP4bb navigation

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

Previous message:
Subject: Re: 3D fitting
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-02-26

Next message:
Subject: Re: units of f0, f', f''
From: Bernhard Rupp br {- at -} RUPPWEB {- dot -} ORG
Date: 2010-02-26