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Re: [modeller_usage] Modelling Asymmetric Unit with Symmetry



Hi.

The software Swiss PDB Viewer (SPDBviewer) has an option to generate copies of your asymmetric or biological unity in any space group you choose. Maybe it can help.

Regards,
 
Flavio Augusto Vicente Seixas
Laboratory of Structural Biochemistry
Department of Biochemistry
Universidade Estadual de Maringá, PR, Brazil
http://www.uem.br

From: Modeller Caretaker <>
To: David Johnson <>
Cc:
Sent: Friday, June 14, 2013 6:10 PM
Subject: Re: [modeller_usage] Modelling Asymmetric Unit with Symmetry

On 6/14/13 9:56 AM, David Johnson wrote:
> I am trying to model a mutation of a molecule whose .pdb file contains
> the asymmetric unit as well as definitions for its symmetry operations.
> I would like to determine the effects on the biological assembly a given
> mutation may have and would therefore like to include the space group
> symmetry in the model. I have looked through the online manual and have
> thus far been unable to produce such a model.

Modeller doesn't have any support for crystallographic symmetry. It
doesn't read the symmetry operations from PDB files, and also has no
support for periodic images or boundary conditions. The closest I think
you can get in Modeller is to use the existing symmetry restraint (see
http://salilab.org/modeller/9.12/manual/node28.html) and make a few
copies of your asymmetric unit, but it'll be expensive because you'll
have to model those copies as well.

    Ben Webb, Modeller Caretaker
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