[Chimera-users] Aligning two residues same name

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 5 10:00:42 PST 2008

> 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

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.

Or, for some quick hints see the examples on the second page of the  
"Quick Reference":

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

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