Dear Professor, Thanks very much for your detailed instruction. If I use rainbow models red,blue then can Chimera produce a color panel to denote the colors used? Thanks Mingjun

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%20Molec...

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.htm...

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