[Chimera-users] Rainbow-coloring

[Elaine Meng]

On Apr 22, 2009, at 9:13 AM, YangMingjun wrote:

> Dear Professor,
>    I am going to use Chimera to plot 20 molecular frames (saved in  
> 10 files with the file name frame_$n.pdb) in one figure and have a  
> question about the color scheme.  I'd like to check the  
> conformational changes from frame 1 to frame 20. Can you please tell  
> me how to color the frames, e.g. with gradual change of each frame  
> in color from red to blue ?
> Does Chimera adopt a default method to color an ensemble of  
> structures when loaded?
> Thanks so much.
> Mingjun
>

Dear Mingjun,
There isn't really a default just for ensembles.  The default behavior  
is to use a different color for each "model" (generally each structure  
file makes one model).  It is in the preferences, New Molecules  
category:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules 
 >

You can use "rainbow" for coloring different models or chains or  
residues, gradually changing from one color to another.  You can use  
either the "rainbow" command or the "Rainbow" graphical interface.

For graphical interface, choose Tools... Depiction... Rainbow.  In  
your case you would want to use the "model" option.  You can change  
the colors by clicking the squares and using the Color Editor.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rainbow/rainbow.html 
 >

Similarly, you could just use the command "rainbow models" to use the  
default coloring, but there are additional keywords to use different  
colors.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html>

For example, if you really only want red->blue and not all the rainbow  
colors in between, the command would be

rainbow models red,blue

Here are the built-in color names:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html#allcolors 
 >

For asking Chimera questions, please send mail to chimera-user at cgl.ucsf.edu 
  and not to me directly, unless you are sending private data.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html