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Re: [modeller_usage] "mutation modelling"
- To: Harsha Balaram <harsha_2kk AT yahoo.com>
- Subject: Re: [modeller_usage] "mutation modelling"
- From: Modeller Caretaker <modeller-care@ucsf.edu>
- Date: Wed, 10 Feb 2010 13:03:16 -0800
- Cc: modeller_usage@listsrv.ucsf.edu
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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