Re: [ccp4bb] NCS and manual building

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

Previous message:
Subject: RAxis & fiber diffraction
From: Sue Roberts suer {- at -} EMAIL {- dot -} ARIZONA {- dot -} EDU
Date: 2008-11-25

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From: Mark Agacan M {- dot -} Agacan {- at -} DUNDEE {- dot -} AC {- dot -} UK
Date: 2008-11-26

Subject: Re: NCS and manual building
From: Prakash Rucktooa p {- dot -} rucktooa {- at -} NKI {- dot -} NL
Date: 2008-11-26

Dear Olga,

I have also encountered the same problem. Find below a script which will
automate the superposition of one protomer onto the others.

Best wishes

Prakash

Superposition script :-

#!/usr/bin/tcsh -f

grep -v -E '^END' Aorig.pdb > new.pdb

rm mat1.mat

foreach chain_name ( B C D E F G H I J )

# Superposition of A on chain_name
superpose Aorig.pdb tot.pdb -s ${chain_name} Aon${chain_name}.pdb
grep
-A 4 Rx >> mat1.mat

# Changing chain name to ${chain_name}
pdbset xyzin Aon${chain_name}.pdb xyzout ${chain_name}.pdb <CHAIN $chain_name
END
eof

grep -E "^ATOM " ${chain_name}.pdb >> new.pdb

rm Aon${chain_name}.pdb

end

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
>

--
_________________________________

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Office : +31(0)205121957
Mobile : +31(0)634454024
e-mail : p.rucktooa@nki.nl
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CCP4bb navigation

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

Previous message:
Subject: RAxis & fiber diffraction
From: Sue Roberts suer {- at -} EMAIL {- dot -} ARIZONA {- dot -} EDU
Date: 2008-11-25

Next message:
Subject: Re: RAxis & fiber diffraction
From: Mark Agacan M {- dot -} Agacan {- at -} DUNDEE {- dot -} AC {- dot -} UK
Date: 2008-11-26