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: