Question: How do I view data in pymol via Ipymol for visualisation in a Jupyter notebook?
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2.3 years ago
M.O.L.S ▴ 30

I am analysing protein data using Python programming language and Jupyter notebook.

In the Terminal I have put an alias in a hidden file on the home directory entitled .bash_profile, in order to be able to open pymol directly from the Terminal .

   alias pymol=/folder/where/pymol/is/located/Applications/PyMOL.app

In Jupyter notebook, the first two commands are executed:

from ipymol import viewer as pymol
pymol.start()

However, the following command gives an attribute error.

pymol.fetch('4MBS') # Fetch PDB

Is there another way to load a file directly from my hardrive for viewing?

The only workaround I have found is using.

import nglview as nv

view = nv.show_file(/path/to/folder/where/protein/located.protein)
view

I appreciate any help in advance as i would like to use pymol in this way, if possible.

Thanks

pymol jupyter python idle • 1.5k views
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