[Chimera-users] using Chimera to superimpose structures using sequence alignments

[Eric Pettersen]

Hi Deepak,
	Well, as long as you have the GUI running the script is pretty simple.  Assuming you have the structures open you want, the script would be:

from MultAlignViewer.MAVIewer import MAViewer
mav = MAViewer(“full-path-to-fasta-file”)
mav.match(mav.seqs[0].matchMaps.keys()[0], mav.seqs[1].matchMaps.keys())
mav.Quit()

This will match the model that auto-associated with the second alignment sequence onto the model that auto-associated with the first sequence, and then exit the MultAlign Viewer instance.

Some notes:

(1) There’s probably a 99.9% chance the structures auto-associate with the correct sequences, but in case you want to be 100% sure, you would provide “autoAssociate=False” to the MAViewer constructor and then call mav.associate(model-to-associate, seq=seq-to-associate-with) to associate each model with the proper sequence.

(2) The matching occurs with default settings.  If you want to use other settings (e.g. iteration/pruning), look at the doc string for the match method in <your Chimera installation>/share/MultAlignViewer/MAViewer.py.  On a Mac, “<your Chimera installation>” is Chimera.app/Contents/Resources.

(3) Presumably you want to do this in a loop.  Look at http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> for the basics of how to do that.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Nov 25, 2016, at 9:41 AM, Deepak Kumar <deepakk1 at andrew.cmu.edu> wrote:
> 
> Hi Dr. Meng & All Chimera Users,
> 
> Regarding the question, yes, I am looking for a script that could superimpose two pdb structures based on a fasta alignment. Please let me know how this could be done.
> 
> Thanks much!
> 
> Deepak
> ________________________________________
> From: Elaine Meng [meng at cgl.ucsf.edu]
> Sent: Friday, November 25, 2016 7:32 PM
> To: Deepak Kumar
> Cc: chimera List
> Subject: using Chimera to superimpose structures using sequence alignments
> 
> Hi Deepak,
> You would still have to show the Chimera GUI (it cannot be done running Chimera with no GUI),  but if you mean using a script instead of interactively choosing menu items, it may be possible.  However, there is no Chimera command to do this.  It would require a Python script.
> 
> For future reference, we recommend sending Chimera questions to the chimera-users at cgl.ucsf.edu list (which I CC’d here, so you do not need to re-send this question).  Since today is a holiday, and I do not know Python, somebody may be able to help you with this question next week.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Nov 24, 2016, at 3:08 PM, Deepak Kumar <deepakk1 at andrew.cmu.edu> wrote:
> 
>> Dear Dr. Meng,
>> I am a Bioinformatician at the Computational Biology Department of Carnegie Mellon University. I have been using Chimera for visualization purposes and for many other of its features. I got to learn about your expertise from here:
>> 
>> http://www.cgl.ucsf.edu/home/meng/index.html
>> 
>> May I please request you to give your suggestions on this problem mentioned below:
>> 
>> I know of one feature "multialign viewer" which uses a fasta alignment file to superimpose two pdb structures in Chimera. However, I have been using this feature through the GUI of Chimera. I am in need of using this feature standalone i.e superimpose two pdb structures based on a fasta alignment file. May I please request you to let me know, how can I perform this step standalone and not through Chimera GUI.
>> 
>> Thank you so much for your time and consideration.
>> Yours Sincerely,
>> Deepak
> 
> 
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