[Chimera-users] Saving Output From Match Align

Eric Pettersen pett at cgl.ucsf.edu
Thu Dec 22 16:43:30 PST 2016

Hi Sanychen,
	Doing exactly what you request is not possible, because Render By Attribute is basically not scriptable.  However, I believe you can get close enough for your purposes.  From your description I’m guessing it’s a Python script.  I sure hope so because what you want is only possible in Python!  Also, from your mail I’m not sure how much of the script you’ve got working so far, but I’m going to guess you’ve gotten the MAV from Match->Align showing and I’ll go from there.
	First you need to find the Multalign Viewer instance that Match->Align created.  This chimera-users message <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html> discusses how to do that.  Also, as mentioned in that message, you should call mav.Quit() when you are done with that particular Multalign Viewer instance.
	Then you need to invoke the “Assess Match” functionality in your MAV instance.  So assuming your reference structure is in a variable named 'ref’ and that your evaluation structures are in a list called ‘evalStructs’ and that you want the resulting attribute named ‘matchDist’, then you would do this:

	mav.assessMatch(ref, evalStructs, “matchDist”)

	Now is when you would have had Render By Attribute write out the matchDist attribute values, but instead you will have to do it “by hand”.  Namely you will have to iterate through the residues of the evaluation structures (i.e. their ‘.residues’ attribute) and for the residues with a ‘matchDist’ attribute (i.e. hasattr(r, “matchDist”) == True) you write the residue and value to a file (“str(r)” will get you a text description of the residue).


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Dec 22, 2016, at 8:11 AM, Muk, Sanychen <smuk at coh.org> wrote:
> Hello,
> I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays.
> Best,
> Sanychen Muk
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