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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