Hello,

I am picking up an old code that used chimera and updating it to use ChimeraX.

Our code writes a python script file that looks like :

import chimera

from chimera import runCommand

runCommand("open ../4ZKC_H_reduce.pdb")

runCommand("swapaa LYS #0:11.B&:LYS lib dynameomics")

runCommand("swapaa TRP #0:51.B&:TRP lib dynameomics")

runCommand("write #0 ../4ZKC_H_reduce.pdb")

and executes

chimera --nogui --nostatus --script python_script.py

I installed ChimeraX on Ubuntu 22.01 with the .deb from your website and "sudo apt install chimerax.deb"

When i execute ChimeraX with my script, i get :

available bundle cache has not been initialized yet

Executing: runscript chim_4ZKC_H_reduce.py

Traceback (most recent call last):

File "chim_4ZKC_H_reduce.py", line 2, in <module>

from chimera import runCommand

ModuleNotFoundError: No module named 'chimera'

Traceback (most recent call last):

File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/scripting.py", line 84, in open_python_script

_exec_python(session, code, argv)

File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/scripting.py", line 61, in _exec_python

exec(code, sandbox.__dict__)

File "chim_4ZKC_H_reduce.py", line 2, in <module>

from chimera import runCommand

ModuleNotFoundError: No module named 'chimera'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 747, in init

run(sess, 'runscript %s' % script)

File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38, in run

results = command.run(text, log=log, return_json=return_json)

File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897, in run

result = ci.function(session, **kw_args)

File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/runscript.py", line 38, in runscript

open_python_script(session, open(script_file, 'rb'), script_file, argv=argv)

File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/scripting.py", line 90, in open_python_script

raise UserError('Error opening python file %s' % stream.name)

chimerax.core.errors.UserError: Error opening python file chim_4ZKC_H_reduce.py

I tried installing chimera using pip but it installs Chimera (the one in python 2.7) and crashes during the installation.

Any ideas on how to fix this? Did i do something wrong somewhere?

Thanks you very much for your help,

Bar Collignon