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

Hi Bar, Glad you were able to figure most things out on your own. In case you haven't figured out this latest one yet, the atom spec "/B:11:lys" means residue 11 in chain B and all lysines in chain B, so you want just "/B:11".

--Eric

Eric Pettersen UCSF Computer Graphics Lab

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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription: