Re: [ccp4bb] Real space rotation translation

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CCP4bb <-- 2008 <-- January 2008 <-- 24 January 2008

Previous message:
Subject: Re: Real space rotation translation
From: Hidong Kim HKim {- at -} DECODE {- dot -} COM
Date: 2008-01-24

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Subject: X-ray Manager/Research Asst. Prof.
From: "David H {- dot -} T {- dot -} Harrison" david {- dot -} harrison {- at -} ROSALINDFRANKLIN {- dot -} EDU
Date: 2008-01-24

Subject: Re: Real space rotation translation
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2008-01-24

Hi Ben,

you can use PHENIX tools for this as well. Example:

phenix.superpose_pdbs fixed.pdb moving.pdb

If no selections provided, then it will use the whole model in
superposition (and do sequence alignment if necessary), or alternatively
it will use selected parts of your model:

phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and
name CA" selection_moving="chain B and name CA"

More details:
http://phenix-online.org/documentation/superpose_pdbs.htm
http://phenix-online.org/

Cheers,
Pavel.

On 1/24/2008 2:24 PM, Hidong Kim wrote:
>
> Hi, Ben,
>
> Try lsqkab. Do a superposition of the before and after coordinates of
> the domain. The log file will have the rotation matrix and the
> translation vector. Good luck,
>
>
>
> Hidong
>
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>
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>
> *Benjamin Brooks *
> Sent by: CCP4 bulletin board
>
> 01/24/2008 01:58 PM
> Please respond to
> Benjamin Brooks
>
>
>
> To
> CCP4BB@JISCMAIL.AC.UK
> cc
>
> Subject
> [ccp4bb] Real space rotation translation
>
>
>
>
>
>
>
>
>
> I was wondering if anyone had a simple way of describing a conformational
> change by measuring the rotational and translational displacement of a
> domain from a starting structure.
> Thank you,
> Ben B
>

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CCP4bb <-- 2008 <-- January 2008 <-- 24 January 2008

Previous message:
Subject: Re: Real space rotation translation
From: Hidong Kim HKim {- at -} DECODE {- dot -} COM
Date: 2008-01-24

Next message:
Subject: X-ray Manager/Research Asst. Prof.
From: "David H {- dot -} T {- dot -} Harrison" david {- dot -} harrison {- at -} ROSALINDFRANKLIN {- dot -} EDU
Date: 2008-01-24