[Chimera-users] Using match

Eric Pettersen pett at cgl.ucsf.edu
Tue Nov 4 15:12:48 PST 2008

Hi Omar,
	If you are using the match command, then there is no way to get that  
information without using Chimera's Python interface.  If, however,  
you use the MatchMaker tool or the mmaker command, you can get a  
sequence alignment of the structures.  That alignment will have a  
highlighted region of the residues used in the final match  
interation.  Clicking on the region will select the residues.  You can  
then use Actions->Write List... to write a list of the selected/ 
unselected residues to a file.
	I can provide guidance on the Python interface if you need to go that  
route instead.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Nov 3, 2008, at 2:53 PM, Omar Davulcu wrote:

> Hi,
> I’m using the match command with a cutoff to align specific regions  
> of related enzymes.  It appears to work fine and remove residue  
> pairs above the cutoff, but is there a way to list those residue  
> pairs which were (or were not) removed?
> Thanks for any help!
> Omar Davulcu
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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