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 Viewer: (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. Example: 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. Elaine 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:

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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