[Chimera-users] Coloring range for residues

Ibrahim Moustafa I.moustafa at psu.edu
Tue Nov 10 10:09:50 PST 2009

Hi Elaine,

  Many thanks for the useful tips and information. What us suggested
definitely helps to highlight the region assumed different conformations
mapped onto a single structure.

 May be I was not that clear in explaining why I asked about the rainbow. I
wanted to be able to follow the conformational change (not just identifying
the region involved in the conformation).

  Surely, what you suggest will be helpful to highlight the region of
conformational changes in a clear way.

  Again, many thanks for your help and for Eric's help.


On 11/10/09 12:52 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

> Hi Ibrahim,
> Just thought I would mention that there are some other interesting
> ways to show conformational changes or conformational variability in a
> single picture.  Some images are attached at the bottom.
> You can assign attributes to residues, and then show those attribute
> values on one or more structures with color and/or "worms". If two or
> more structures are associated with an alignment and you show the
> alignment "RMSD" header, that automatically creates the residue
> attribute named mavRMSD, where the values are the alpha-carbon RMSDs
> for residues in the same column of the alignment.  If you only have
> two structures it boils down to the CA-CA distance between the two
> residues in each column of the alignment.
> You are probably thinking "but I don't have an alignment!" -- however,
> in Chimera it is easy to make one.  If you have > 2 structures already
> superimposed, you can use Match->Align (under Tools... Structure
> Comparison) to create and display the sequence alignment.  If you have
> 2 structures, you can use MatchMaker to both create the pairwise
> sequence alignment and superimpose the structures.
> Here is an example with a G protein in the "on" and "off"
> conformations, using the command version of MatchMaker:
> open 1tad
> open 1tnd
> del ~ :.a
> mm #0 #1 show true
> That will create the pairwise sequence alignment with RMSD header
> shown.  Then in the alignment window, choosing "Structure... Render by
> Conservation" brings up the dialog for mapping colors and/or worm
> fatness onto the structures.  In that dialog, change the attribute
> from "mavConservation" to "mavRMSD" to see the histogram of values.
> Then use the Colors or Worms section in the dialog to map the values.
> You can do it for either or both structures.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#r
> ender 
> I attached images for the example above, where mavRMSD is shown with:
> (a) worms for both structures
> (b) color on one structure
> (c) both color and worms on one structure
> You could also do the coloring with command "rangecolor" instead of
> with the dialog
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
> The example uses two conformations of the same protein, but it will
> also work with different proteins along as they are similar enough for
> Matchmaker to create a good alignment.
> Or instead of using an alignment, you can create your own attribute in
> a text file and then use "rangecolor" or the "Render by Attribute"
> tool (under Tools... Depiction), actually the same dialog used above
> for showing mavRMSD, to show your custom attribute on the structure.
> There is a description of the file format
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/definea
> ttrib.html#attrfile
> and example files
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/definea
> ttrib.html#examples
> Probably more information than you wanted  8-)
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco

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