[Chimera-users] Coloring range for residues

[Elaine Meng]

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#render 
 >

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/defineattrib.html#attrfile 
 >
and example files
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.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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