[Chimera-users] Conserved amino acids

[Elaine Meng]

Just to add to Rebecca's excellent answer:

(A) You might already have a sequence alignment file.  It could be just those 5 sequences, or a different set: whichever alignment you want to use to define "invariant."  The only requirement is that the structure you want to color is associated with one of the sequences in the alignment.  You would just open the sequence alignment file and the structure file in Chimera, and check for association.

Multalign Viewer will automatically show the contents of a sequence alignment file opened in Chimera.  Usually sequence-structure association happens automatically, but if not, you can specify association manually.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association>

(B) There are several options for calculating values in the "Conservation" line above the sequences. AL2CO is one option.  This is set by choosing from the sequence window menu "Preferences... Headers" and specifying "Conservation style"
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavpref-structure>

The AL2CO measures are probably best if you care about a range of values.  However, if you only need a simple measure, % of column with the most prevalent residue at that column, you can use the residue attribute named mavPercentConserved.  For example, commands:

show :/mavPercentConserved>75
color orange :/mavPercentConserved>75
color red :/mavPercentConserved=100

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavAttributes>

Or for gradual shading like the Render by Attribute tool that Rebecca mentioned (see sequence window menu: Structure... Render by Conservation), you could also use the command "rangecolor"
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>

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 17, 2013, at 6:33 AM, Rebecca Swett wrote:

> Use match-> align to get a structural superposition and sequence alignment, then set your alignment type to AL2CO. Go to render by attribute and then hit the select by attribute tab. Select the range from 0-whatever your maximum is. Should be around 4 if you've got any conserved tryptophans. That will select all invariant residues. 
> 
> Jean-Paul Boissel <boissel at uni-mainz.de> wrote:
> Hi, 
> By homology modelling, I got putative structures for five closely related amino acid transporters.  Is there any script that will allow the quick selection and visualisation of the invariant residues on the structures?
> Thanks,
> Jean-Paul
>