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

[Tom Goddard]

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']
t.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]])

  Tom



> 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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