[Chimera-users] Evolutional-based analysis in Chimera

[Elaine Meng]

Hi Gleb,
Chimera doesn’t have evolutionary trace, other than your manually doing something similar with related tools in Chimera, some of which I mention below:

What you can do is open a sequence alignment and calculate conservation in the columns (various methods available, see AL2CO Conservation in Multalign Viewer).  The conservation values per alignment column are automatically assigned as attributes to any structure residues associated with the alignment.  You can color them by the values using Render by Attribute or command “rangecolor.”

You would have to generate or already have the appropriate sequence alignments.

Multalign Viewer manpage, see the sections on Preferences, Headers (how to calculate Conservation) and Residue Attributes (coloring to show the conservation values):
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>

See also the “Sequences and Structures” tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>

If you wanted average conservation in the interface: if you have somehow selected the interface residues in the structures (for example with Find Clashes/Contacts to find residues near “the guy") you can use Attribute Calculator to calculate average conservation over just those residues.  Attribute Calculator manpage and tutorial with example of using it:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html>

You could also just get average conservation of the non-interface residues (after inverting the selection), or only surface residues (after showing surface, use Select by Attribute to only select those with surface area greater than some cutoff) or average over the whole protein (not using a selection).

If you want to calculate surface area of the interface, see command “measure buriedArea”.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>

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 May 25, 2016, at 6:12 AM, James Starlight <jmsstarlight at gmail.com> wrote:

> Dear Chimera Users!
> 
> For my particular analysis I have 2 homologue membrane proteins (one
> is bacterial, and another one- mammalian cytocrome-C oxydase) each
> bound to same smaller (ligand) protein called for simplicity
> "the_guy". For that particular case the conservation in sequence of
> both protein is quite low however 1) the overall fold of both proteins
> especially within the membrane-embedded region as well as 2)
> ligand-bound (which is mostly the water exposed loops) region are
> quite similar.
> Now using some Chimera  tool I need to estimate binding interfaces of
> two homologous proteins  in terms of the conservation of the resides
> involved in binding of the_guy. Then I need to make more complex task-
> performing the same evolutional analysis but comparing 2 ensembles
> extracted from the MD trajectory represent simulation of binding of
> each of the protein with the_guy to track correlations of the
> statistics between the residues involved in the binding during MD as
> well as overall conservation for particular fold. Does the
> "Evolutionary tracing" might be useful here?
> 
> Thanks for help!
> 
> Gleb