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

[Elaine Meng]

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
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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