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 


The answer to this question is that a  bash shell .pml script needs to be made instead of a python .py script. 

The shell script can be shown in a Jupyter Notebook by using RawNBConvert setting, which is found underneath the help menu. 

The images generated from the .pml script can be viewed using Pymol and snapshot  jpeg or png files can be taken of the molecules. 

The ipymol does not work and the nglview is not required. 