"Mutating" a residue requires at least a rotamer library so that the residue
conformation minimizes energy. I don't think that Jmol has this capability
(minimization in Jmol is designed for small molecules).
You should consider other packages. I don't know about Pymol (which scripts can
now be read by Jmol), but I've used UCSF Chimera for that purpose.
Paul
Le 08/08/13, Amjad Farooq <am...@farooqlab.net> a écrit :
> Hi Jeff,
>
> Thanks for your response.
>
> I fully agree--ideally one needs an NMR or x-ray structure to compare
> structural changes in wildtype versus mutant protein.
>
> However, it is sometimes useful to mutate a residue on-the-fly to demonstrate
> to novices how such a mutation might create a lethal cavity that will likely
> affect protein structure and subsequently its catalytic (if the mutation is
> located within or near active site) or binding capacity (if the mutation is
> near a binding interface).
>
>
> You understand what I mean. Of course, one could model the mutant protein but
> that can be cumbersome if you are working with lots of mutations or lots of
> proteins as I do in collaboration with genomicists.
>
> There must be a way to mutate a residue in JMol. I know that PDBViewer can do
> it but I would prefer to work with a browser-driven software such as JMol
> that I can also share with my collaborators.
>
>
> Thanks for your help!
>
> AMJAD FAROOQ PhD DIC | Associate Professor
> Dept of Biochemistry & Molecular Biology | Miller School of Medicine |
> University of Miami | Miami | FL 33136
>
> Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami , FL
> 33136
> am...@farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955
> | www.farooqlab.net(http://www.farooqlab.net)
>
>
>
>
>
>
> On Thu, Aug 8, 2013 at 11:46 AM, Jeff Hansen <jhan...@depauw.edu> wrote:
>
> > Compare how? Do you want to see how the mutation affects the structure?
> > Really need and X-ray or NMR structure of each for that to have any real
> > meaning.
> >
> >
> > ***********************************************
> > Jeff Hansen, Professor and Chair
> > Department of Chemistry and Biochemistry
> > DePauw University
> > 602 S. College Ave.
> > Greencastle, IN 46135
> > jhan...@depauw.edu
> > ***********************************************
> >
> >
> >
> > On Aug 8, 2013, at 11:32 AM, Amjad Farooq <amja...@gmail.com> wrote:
> >
> >
> >
> >
> > > Hi guys,
> > >
> > > Is it possible to mutate an amino acid in JMol.
> > >
> > > For example, how can I introduce the K63A mutation (mutate lysine 63 to
> > > alanine) into my protein to compare wildtype versus mutant?
> > >
> > > What is the JMol command?
> > >
> > > Thanks!
> > > Amjad
> > >
> > >
> > >
> > >
> > >
> > >
> > >
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