On Dec 21, 2009, at 5:14 PM, gytjyb wrote:
hello:meng! thank you for your help! i want to make a surface about protein. i want to do lipophilicity and electrostatics surface,we had better label some amino acid on the surface,how can i do? or i just use differrent color for different amino acid category. i think the color must be very different from each. so i can recognize each other,and find out some important different between homology protein. thank you very much!
Hello, It is better to send Chimera questions to chimera-users@cgl.ucsf.edu (instead of to me directly) and include a short description in the "Subject" line. You can show lipophilicity on the surface with menu item "Presets... Interactive 3 (hydrophobicity surface)" where orange is most lipophilic and blue is most hydrophilic. You can show Coulombic electrostatic potential on the surface with "Tools... Surface/Binding Analysis... Coulombic Surface Coloring" The regular labels are not that good when you are showing a surface. They are usually partly inside the surface so you can't read them. If it is for a figure, you can put labels anywhere you want with "2D Labels" (under Tools... Utilities), but those do not move when you rotate the structure. Also, there are pop-ups that say what is under your mouse, but they only show the detailed information when you are not showing the surface. Sometimes I like to use color-coding, a different color for each amino acid type. Of course, you can't have that as the same time as the lipophilicity or electrostatic coloring. There is a command file (rescol.com) linked to the User's Guide that does my favorite residue color-coding: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile
You would save that file to your computer as plain text and just open it (file named *.com) in Chimera to apply the residue color-coding. 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