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@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@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
>
>

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