Re: [ccp4bb] Building structure in COOT

- Protein crystallography

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

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Subject: Choosing weighing term
From: conancao conan_cao {- at -} HOTMAIL {- dot -} COM
Date: 2009-04-01

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From: Alexei Vagin alexei {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-04-01

Subject: Re: Building structure in COOT
From: David Cobessi David {- dot -} Cobessi {- at -} IBS {- dot -} FR
Date: 2009-04-01

Liew Chong Wai wrote:
> Hi,
>
> Good day
> I am currently building my structure by using COOT. My protein is a
> tetramer protein and I have fit my protein sequence into one of the
> monomer of the homologous model. May I know how can I replace
> other monomer with the amended monomer??
> Thanks
>
> *Chong-wai*
>
Hi Chong-wai,
Several possibilities to generate the tetramer from the monomer, let say A.
You can calculate the RT matrices ( in CCP4 or using LSQMAN and MOLEMAN2
or using O for example) to superpose the monomer A onto B, C and D and
then apply these matrices to the amended monomer (A) in order to
generate the tetramer.
You can also superpose the monomer A onto B in COOT by using SSM or LSQ
and save the new position as monomer B in COOT.... etc... and then you
can generate 4 monomers and the tetramer. Do not forget to change the
chain ID before refinement.
Best regards,
David

--

David Cobessi
Institut de Biologie Structurale
41, Rue Jules Horowitz
38027 Grenoble Cedex-1, France
Tel:33(0)438789613
33(0)608164340
Fax:33(0)438785122

CCP4bb navigation

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

Previous message:
Subject: Choosing weighing term
From: conancao conan_cao {- at -} HOTMAIL {- dot -} COM
Date: 2009-04-01

Next message:
Subject: Re: Error with molrep when using locked srf.
From: Alexei Vagin alexei {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-04-01