I have been using Chimera to generate the colorful ribbon picture for the pdb file using command line. Now I am tring to figure out the general way of defining the bfactor range corresponding to the different colors. I found the flexible python code for making the rainbow color by bfactor and tried it out. But it ended up with the file/open error message as I didn't see any problem in the code.

Dear Li, In more recent versions of Chimera (yes, we do recommend getting 1.2065), there are easy ways to color by B-factor that do not require making a python script.

First, there is the tool Render by Attribute, which shows the B-factor values on a histogram. You can put as many colored sliders as you want on the histogram to define the coloring. If you want to color the ribbon, you need to change to residue attributes and then pick the average B-factor as an attribute (since the ribbon can only have one color per residue, not per atom). See the man page at http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html

Second, there is the command "rangecolor," which also colors according to attribute values (the B-factor is just one of many attributes). It depends whether you prefer the graphical interface or typing commands. See the man page at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html

I didn't look at your script, but I think these are much nicer ways of showing numerical values on the structure. I hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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