Re: [modeller_usage] "mutation modelling"

On 02/10/2010 02:30 AM, Harsha Balaram wrote: > I would like to know the python scripts used to model mutant sequences > of a known structure.

See http://salilab.org/modeller/wiki/Mutate%20model

> Is the "model-default" script advisable for mutants with high structural > variations?

Regular comparative modeling, by construction, will yield models that are structurally similar to the templates, so if you are expecting a large structural change, you won't see it using "model-default". The script in the wiki is not using distance-based (homology-derived) restraints, and allows the SNP to relax using only CHARMM and dihedral forcefield terms.

Ben Webb, Modeller Caretaker