[Chimera-users] Aligning two residues same name

[Elaine Meng]

> 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 at 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