Re: [modeller_usage] "mutation modelling"

[Modeller Caretaker <>]

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
--
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