Hello,

I would like to use the Matchmaker comparison in ChimeraX (specifically the 'across all' RMSD value given) to compare 10,000+ structures so I would like to incorporate it into a python script in a jupyter notebook. I am very familiar with scripting with python in jupyter notebooks but I am not as familiar with getting two scripts to work together as appears to be needed to use matchmaker in an existing jupyter script.

The script I am attempting to use is found below. I wrote it following some of the guidance in your documentation.

```

#Chimera Command Line

import chimera

import os

from chimera import runCommand as rc # use 'rc' as shorthand for runCommand

from chimera import replyobj # for emitting status messages

file1='C:/Users/jamie/Downloads/temppdb1.pdb'

file2='C:/Users/jamie/Downloads/temppdb2.pdb'

structure1=rc("open " + file1)

structure2=rc("open " + file2)

rc("mmaker structure1 structure2")

```

I get the error 'No chimera module'

I try to install chimera using 'pip install chimera' and it won't install.

Can you offer any guidance on getting this to work?

Best,

Jamie Dixson