Paul,
Thanks for your input. But, I do not believe Chimera is a web-based
application. I am looking for a web-based application to perform mutations.
Amjad
On Thu, Aug 8, 2013 at 1:19 PM, Pillot Paul <paul.pil...@ac-orleans-tours.fr
> wrote:
> "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*
>
>
>
>
> 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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