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insilichem / scripts

Miscellaneous collection of molecular modelling scripts
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multisite.py #1

Open Lrolmar opened 5 years ago

Lrolmar commented 5 years ago

I run this script in the conda environment Insilichem (where gaudi runs normally).

The following error pops-up:

TypeError: name already defined

  File "/home/lroldan/.local/UCSF-Chimera64-1.13.1/share/chimera/__init__.py", line 2439, in initializeGraphics
    initializeColors(nogui)

See reply log for Python traceback.

Then, if the line "pychimera.enable_chimera()" is commented out in the script, the following error appears:

ImportError: No module named gaudi.box

  File "/home/lroldan/Master/Metals_bA/Scripts/multisite.py", line 57, in <module>
    from gaudi.box import open_models_and_close

See reply log for Python traceback.
jaimergp commented 5 years ago

Seems like you are initializing Chimera twice. I think that multisite.py handled initialization on its own (look at the top of file for pychimera imports), so there's no need to execute it with pychimera again. That way, we can later use multiprocessing in a simpler way.

So, if my guess is correct, just use python multisite.py.

Lrolmar commented 5 years ago

Then the following error appears:

ImportError: No module named gaudi.box

File "/home/lroldan/Master/Metals_bA/Scripts/multisite.py", line 57, in
from gaudi.box import open_models_and_close

See reply log for Python traceback.
jaimergp commented 5 years ago

Can you execute that same line (57) on its own, in an interactive pychimera session?

$ conda activate insilichem
$ pychimera
>>> from gaudi.box import open_models_and_close

Also, please use Markdown formatting to, at least, enclose code blocks in triple back-ticks.