[Chimera-users] Using match

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 4 17:00:14 PST 2008

Hi Omar,
Just wanted to add a little more discussion on the matching methods  
(possibly more information than you wanted!):

- Matchmaker only uses one atom per residue (CA for amino acids),  
whereas match can use whatever atoms you specify, as long as there are  
equal numbers of atoms from the two structures

- however, if the main reason you were using match instead of  
matchmaker was to include only parts of the enzymes instead of their  
full sequences, you can also do that with Matchmaker and Multalign  

   (a) Perform an initial round of matching just to get the sequence  
alignment: use Matchmaker with iteration/pruning turned off and  
showing the sequence alignment turned on (GUI and command both have  
these options).  This displays the pairwise sequence alignment and  
uses all aligned pairs to superimpose the structures. Keep this  
alignment open.
Example commands:
open 2mnr
open 4enl
preset apply int 1
mmaker #0 #1 iterate false show true

   (b) In the alignment, draw box(es) for the segments you want to  
consider in the match:  If it is a single contiguous region, you can  
simply drag to create that box.  If there are disjoint parts, you  
would need to use Shift-drag so that the separate boxes would still  
belong to the same region.  The corresponding parts of the structures  
will become selected in the main Chimera window.
I only want to use the N-terminal domains of these enzymes, approx up  
to 2mnr residue 127, so I drag a box from the beginning of the  
sequence alignment to position 150.

   (c) Perform another match with iteration considering only the boxed  
segment(s): In the Multalign Viewer (sequence alignment) window,  
choose "Structure... Match" - in the resulting dialog, turn on "Match  
active region only", "Iterate..." with the desired cutoff, and "Create  
region showing matched residues".  After OK/Apply, there will be light  
orange boxes that you can click on and proceed as described by Eric.


On Nov 4, 2008, at 3:12 PM, Eric Pettersen wrote:

> 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
> 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

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