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

Deepak Kumar deepakk1 at andrew.cmu.edu
Fri Nov 25 09:41:36 PST 2016

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!

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.
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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