I don't know of a non-cumbersome way. If you are adept at Python programming, the function that the match command calls is Midas.match(), defined in that module's __init__.py file, and you could lift the code that does the match and computes the matrix from there. The Midas module is found in <your Chimera installation>/share/Midas on Windows/Linux and in Chimera.app/Contents/Resources/share/Midas on Mac.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Oct 5, 2021, at 6:35 AM, Engeholm, Maik via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi there,

I'm trying to superimpose two models from inside a python script and get back the transformation matrix. I know I can do something like

chimera.runCommand("match #1 #0 showMatrix true")

but then the matrix is written to the ReplyLog. (Of course I could save the ReplyLog and then read it in from my script to access the matrix, but that seems quite cumbersome.) Is there a better way to do this?

Cheers,

Maik

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