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 modeller-care@salilab.org To: David Johnson da.johnson.a@gmail.com Cc: modeller_usage@salilab.org 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