Hi Hernando,

This old chimera-users message shows how to find the alignment in Python and save it: [Chimera-users] easy way to make alignments in chimera. You can’t do it in nogui mode since the MAV window has the alignment data. You would be able to do it in nogui mode in ChimeraX, but the code would be significantly different of course.

Anyway, if you are doing this in a loop you may want to call mav.Quit() after saving your alignment in order to quit MAV and conserve memory.

—Eric

Eric Pettersen

UCSF Computer Graphics Lab

On May 3, 2019, at 2:03 PM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:

Dear Chimera,

Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script?

Thanks

H.

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