[Chimera-users] superimpose models from inside a python script and access the transformation matrix

Tom Goddard goddard at sonic.net
Wed Oct 6 11:26:19 PDT 2021

ChimeraX is much better than Chimera at giving you results from commands in Python.  For instance, in ChimeraX

open 1a0m
open 1a0m

Then using ChimeraX Python shell (menu Tools / General / Shell):

from chimerax.core.commands import run
results = run(session, 'match #1/A to #2/B')
t = results[0]['transformation matrix']
-> array([[ -0.31727375,  -0.30378517,  -0.8983607 ,  27.04037902],
       [ -0.31084291,   0.92828353,  -0.20412344,   2.9200737 ],
       [  0.89594311,   0.21448605,  -0.38894946, -10.81923792]])


> On Oct 6, 2021, at 9:18 AM, Eric Pettersen via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hi Maik,
> 	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 at cgl.ucsf.edu <mailto:chimera-users at 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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