On Jul 12, 2023, at 7:43 AM, Collignon, Bar /FR via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Once again, i apologise for the continuous spams with useless questions. It is hard to differentiate between Chimera documents and ChimeraX. 

I have succeeded in applying rotamers using 

swapaa /B:51:TRP TRP rotLib dynameomics

and 

swapaa /B:11:lys lys rotLib dynameomics

My problem is now that all of my lys get rotated instead of just one. But i will work on it and stop sending you mails...

Once again, please disregard my previous mails. 

Have a good day 

Bar Collignon

---

De : Collignon, Bar /FR <Bar.Collignon@sanofi.com>
Envoyé : mercredi 12 juillet 2023 12:28
À : chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Objet : RE: Problem using a python script to run chimeraX (installation?)

 

Im sorry for my previous mail, i found the problem myself and using your extensive documentation. 

I do run into another problem : 

swapaa LYS #0:11.B&:LYS lib dynameomics

which seems to still be how you run swapaa, says that "LYS" is not a valid residue. "lys" as well and i tried other residues as per your examples (thr, leu, tyr) and i get the same error everytime 

swapaa LYS #0:11.B&:LYS

.......^

Missing or invalid "residues" argument: invalid residues specifier

Thank you for your help 

Bar Collignon

---

De : Collignon, Bar /FR
Envoyé : mercredi 12 juillet 2023 12:02
À : chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Objet : Problem using a python script to run chimeraX (installation?)

 

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

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