[Chimera-users] Ribbon gradient coloring

[Elaine Meng]

Hi Vamsee,
You can assign "attribute" values to the residues 
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html>

... then map attribute value to colors using "Render by Attribute" or command "rangecolor"
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>

It depends what you mean by gradient:  While the mapping of values to colors is continuous (colors will be interpolated), the ribbon "piece" for each residue is only a single color, so you will see color boundaries between residues unless their values are very similar.

For example, the following command would color a ribbon by the built-in attribute named kdHydrophobicity (amino acid hydrophobicity on the Kyte-Doolittle scale).  Values -4 and lower would be shown with lime green, then up to 0 gradually interpolated to white, then up to 4 r  interpolated up to orange.  

rangecol kdHydrophobicity,r -4 lime green 0 white 4 orange

There is a simple format for reading in your own custom attributes:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>
... or if you have only a few values to assign, you can do them one at a time with command "setattr":
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

See also tutorials, including:

B-factor coloring
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html>
Surface properties
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
Attributes
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.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 Sep 10, 2012, at 12:59 PM, vamsee wrote:

> Hi All,
> Is there a way to color the ribbon with a gradient? In my case, it has to be an increasing and then decreasing gradient. Ex: Let's say I have data that shows that a certain region of a protein is highly dynamic. This region consists of approx 11 residues and the most dynamic region in these 11 are the residues 5,6 and 7. Now, I need to color the ribbon in such a way that residues 1 and 11 are the same color (green), 2 and 10 (yellow), 3 and 9 (light orange) 4 and 8 (orange) 5,6 and 7 (red). I could do this by coding it but it becomes a step gradient and it doesn't look so good plus if I need to do this for residues in a bunch of proteins/peptides, the task quickly becomes tedious. I would rather write 2 lines of code for the complete protein than write 1 line/residue/protein. Any ideas? 
> Thanks in advance
> Vamsee