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:

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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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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