Re: [ccp4bb] NCS and manual building

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

Previous message:
Subject: NCS and manual building
From: Olga Boudker olb2003 {- at -} MED {- dot -} CORNELL {- dot -} EDU
Date: 2008-11-25

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Date: 2008-11-25

Subject: Re: NCS and manual building
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-11-25

Use Coot
option 1)
rebuild your chain A and superimpose manually with Coot A to the other
chains, then write out a new merged PDB file
option 2)
use the Coot command which allows you to copy whatever you have
modeled in one chain to the other chains.
for more info check out the link:
http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC136
option3)
since your NCS operators won't change by much you can generate a
script using Moleman - but option 1+2 are easier

Jürgen

On 25 Nov 2008, at 11:18, Olga Boudker wrote:

> Dear all,
> I am working with a relatively low res. crystal structure with
> multiple protomers in the asymmetric unit related by NCS. I am
> currently running rounds manual model building in Coot and
> refinement using Refmac5. Could anybody suggest a shortcut for the
> following procedure: I start with an initial model containing all
> protomers; generate NCS operators for A to B, A to C et c.; rebuild
> protomer A; use the operators and the rebuilt A to generate all
> other protomers; and combine them all in a single pdb file.
> Currently I do all that manually using lsqkab and text edit and it
> is really painful. Is there an available routine to do this? For
> various reasons I would like to stick with Refmac5 rather then CNS,
> in which of course the symmetry would have been easier to implement.
> Many thanks,
> Olga
>
> --

-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

CCP4bb navigation

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

Previous message:
Subject: NCS and manual building
From: Olga Boudker olb2003 {- at -} MED {- dot -} CORNELL {- dot -} EDU
Date: 2008-11-25

Next message:
Subject: MOSFLM error message reading RAxis IV++ image
From: Roger Rowlett rrowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2008-11-25