Re: [ccp4bb] NCS and manual building

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

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From: "Jens T {- dot -} Kaiser" kaiser {- at -} CALTECH {- dot -} EDU
Date: 2008-11-28

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Subject: Re: NCS and manual building
From: "Jens T {- dot -} Kaiser" kaiser {- at -} CALTECH {- dot -} EDU
Date: 2008-11-28

MAIN does that for ages (n_molecules->generate_others). Also, the new COOT can
do that (look in the - rather cluttered - treasure
chest 'Extensions'->'NCS'->'Copy NCS chain')

HTH

-j.

On Wednesday 26 November 2008 00:25:12 Prakash Rucktooa wrote:
> 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

CCP4bb navigation

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

Previous message:
Subject: Re: soft white paraffin
From: "Jens T {- dot -} Kaiser" kaiser {- at -} CALTECH {- dot -} EDU
Date: 2008-11-28

Next message:
Subject: Re: Program to fill unitcell randomly
From: "Ralf W {- dot -} Grosse-Kunstleve" rwgk {- at -} YAHOO {- dot -} COM
Date: 2008-11-29