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@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@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
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@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@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@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
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@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@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@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@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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participants (3)
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Deepak Kumar -
Elaine Meng -
Eric Pettersen