[Chimera-users] matching using parts of structures

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 20 14:39:07 PDT 2010

Hi JD,
Matchmaker (mmaker) figures out the pairing between the two structures itself, by making a sequence alignment based on the residue types and secondary structure.  Currently it uses whole chains to make the alignment, so you can only specify whole chains in the mmaker command.

If you want to only use parts of the chains, here are some possibilities that can be done now:

(a) use the "match" command, which requires specifying the pairing yourself by giving the residues in the two structures in the same order.    Can be very tedious if there are lots of residues you want to use.

(b) use a two-step process.  First use mmaker with "show true" or the similar option in the GUI to display the pairwise sequence alignment.  Second, use only some part of that alignment to superimpose the structures.  You would do that by using the mouse in the alignment window to drag a box or boxes containing only the part you want to use for superposition.  If you want more than one box, use Shift-drag to start each one, so that they will all be considered together during the match.  Then from the sequence window menu use "Structure... Match" with "Match active region only" turned on. You might want to try some of the other options too, such as "Iterate..."  This all assumes you agree with the alignment you get in the first step.

(c) this is the most hack-y but perhaps will work... delete all of the structures except the parts you want to use for mmaker, then apply mmaker.  Open new copies of each structure with all their original atoms and then superimpose each copy on its fragment using the "matrixcopy" command.  Then close the partial models, leaving only the full models in the desired positions.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 17, 2010, at 8:28 AM, Jean Didier Pie Marechal wrote:

> Hi again,
> I'd like to do a mmaker for a region of space leading to something like this:
> mmaker #(ref-model and part of the selection) #(flex-model and part of the selection)
> So far I haven't found the correct syntax to do so but I am pretty sure we can do that.
> any help?
> Cheers
> JD

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