Changing residue name works. Deleted membrane, saved pdb without membrane. Loaded the two models. Command line: match :XXX :YYY

Hi Francesco, You can still use the name without changing it, for example open 4hhb open 4cpp preset apply interactive 1 match #1:hem #0:hem.a ~ribbon This matches the single heme residue of 4cpp (#1) to the chain A heme of 4hbb (#0 - it has four heme residues, in chains A-D). The protein parts are totally different but I just used this as an example because they both have heme. It takes a little time, but I recommend learning about the command- line specification language because it is used in so many commands, and can be very powerful yet flexible. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html Or, for some quick hints see the examples on the second page of the "Quick Reference": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/quickref.pdf Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html