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 .
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.