On Mar 4, 2015, at 10:14 AM, Nishant Ray Velagapudi <nishray@uw.edu> wrote:

Hello Mr. Petterson,

I was looking for some help with using UCSF chimera and I was wondering if I can directly email you my question. If this is not the appropriate address, my apologies, and could you point me in the appropriate direction for support?

Hi Nishant, You should probably send questions like these to the chimera-users mailing list. That way other people can benefit from the answer, and it also allows others to answer in the cases where I'm not really the best person for the question.

My issue is that I want to automate the process of creating and saving structure based sequence alignments. It has been simple to open the file and align them, but I am not sure how to save the .fasta alignment file out. Here is what I have so far:

for fn in file_names: replyobj.status("Processing: " + fn) rc("open " + fn) rc(mm #0 #1 show true) rc("close " + fn)

The bold line is the problematic one - is there any way to write out the resulting alignment file in a programmatic fashion?

Yes. You can locate the MultAlign Viewer (MAV) instance using the code in this previous chimera-users mail: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html That message also describes how to save the alignment to a file, in conjunction with the info in this message: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010015.html You can search the chimera-users list from this page to see if your question has been asked previously: http://www.cgl.ucsf.edu/chimera/docs/feedback.html I hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu