[Chimera-users] Analysis of the multiple alignments + structures

James Starlight jmsstarlight at gmail.com
Mon Sep 1 00:36:44 PDT 2014


Thanks alot!!

James


2014-08-29 19:43 GMT+02:00 Elaine Meng <meng at cgl.ucsf.edu>:

> Hi James,
> These tutorials may also be worth a look, or at least a glance to see if
> they cover things you want to know about:
>
> Structure Analysis and Comparison
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
>
> Functional Annotation Scenario: The Structure-Function Linkage Database
> (SFLD) and Chimera
> <http://www.rbvi.ucsf.edu/chimera/data/sfld2014/sfld2014.html>
>
> Elaine
>
> On Aug 29, 2014, at 10:23 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> > Hi James,
> > It happens that I just finished making a new online tutorial “mapping
> sequence conservation onto structures with Chimera”!!
> >
> > <http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html>
> >
> > The tutorial has  lots of links and details.  I’m not aware of plugins,
> but Chimera’s Multalign Viewer is very rich in features for this type of
> work; it includes a variety of options for calculating and displaying
> conservation, mostly provided via the included AL2CO program from the
> Grishin group. Anyway, that and much more is described in the new tutorial
> and links therein.
> >
> > Some of the tutorials in the User’s Guide (included with Chimera
> download) also address this area, with a bit less detail:
> >
> > Sequences and Structures: <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>
> > Superpositions and Alignments: <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html
> >
> >
> > Of course, besides the sequence-related features, you could still use
> general structure analysis (H-bonds, Rotamers, etc.) to investigate your
> sequence-structure hypotheses.
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > On Aug 29, 2014, at 3:52 AM, James Starlight <jmsstarlight at gmail.com>
> wrote:
> >
> >> Dear Chimera Users!
> >> I'd like to perform analysis of the set of the sequences (presented in
> the FASTA multiple-alignment file) together with the some (not all) X-ray
> structures available for several of the sequences presented in its database
> to detect conservative motifs (from sequence) and make conclusions about
> its functional importance (based on the analysis of the Xray data) to make
> conclusions between conservation of sequence and it's functional relevance.
> Could you provide me with the some useful Chimera plugging as well as for
> some tutorials
> >> Kind regards,
> >> James
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
>
>
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