Must run pymol -R -cKRQ to use ipymol

[celine168]

Hello! I ran these commands to install pymol and ipymol:

conda install -c schrodinger pymol
pip install git+https://github.com/cxhernandez/ipymol.git@2a30d6ec1588434e6f0f72a1d572444f89ff535b

I tried the example code, but calling pymol.start() would stall. The rest of the code wouldn't execute unless if I called pymol -R -cKRQ in a Terminal in JupyterLab.

from ipymol import viewer as pymol
pymol.start()   # Start PyMOL RPC server
pymol.fetch('3odu') # Fetch PDB
pymol.show_as('cartoon') # Show as cartoon
pymol.bg_color('white') # Set background color to white
pymol.display() # Show current display

Not sure if this is intended behavior. I expected the rest of the code to execute without opening up the Terminal.

[MooersLab]

Thank you for this post.
I installed ipymol using the pip at the PyMOL prompt inside an open PyMOL session.

I had success by

• making a kernel for the python interpreter inside the schrodinger PyMOL
• making a bash alias to this pymol
• running it in a terminal opened with the jupyter notebook using the command

pymol -Rq 

so that the pymol session is interactive.

I found that I had to use do in place of cmd in my python code.