(The pymol commands contains content from http://pymolwiki.org/index.php/Gallery ), with my modification (quantaosun@gmail.com).

This notebook is tricky! Make sure you use it inside the github directory like C:\Users\yournamexxxxxx\Desktop\jupyter-demo\ipymol-master. The server status should be http://localhost:8888/tree/ipymol-master

You should download the github repository https://github.com/cxhernandez/ipymol to your local laptop, then start the notebook inside the repository. You can do this by starting up a new Anaconda prompt shell, then use cd "C:\Users\yournamexxxxxx\Desktop\jupyter-demo\ipymol-master" to go inside this folder, then type "jupyter notebook" to start the jupyter notebook in a local server mode.

#wget https://github.com/cxhernandez/ipymol.git
wget https://github.com/cxhernandez/ipymol

pip install numpy

pip install matplotlib

pip install ipython

pip install pillow

You should have already installed the open sourecd pymol before move on.

%pylab inline
from ipymol import viewer as pymol

pymol.start()

If you encounter problem in the next line, you need to double check where you are by "pwd", and please make sure you are in the right layer of the github directory, which should be "ipymol-master".

pymol.fetch('4MBS')

'4MBS'

pymol.remove('chain A')
pymol.remove('solvent')

pymol.select('ligand', 'resn MRV')
pymol.show_as('sticks', 'ligand')
pymol.show('spheres', 'ligand')
pymol.set('stick_radius', '.07', 'ligand')
pymol.set('sphere_scale', '.25', 'ligand')
pymol.set('sphere_quality', '4', 'ligand')

pymol.show_as('spheres', '4MBS and not ligand')
pymol.set('sphere_transparency', '.2', '4MBS and not ligand')

pymol.center('ligand')
pymol.orient('ligand')
pymol.zoom('ligand', '10')
pymol.do('rotate z,180; rotate x,90;')
pymol.center('ligand')
pymol.clip('near', '5')

pymol.bg_color('white')
pymol.do('util.cbaw;')
pymol.color('slate', 'elem N')
pymol.set('light_count', '8')
pymol.set('spec_count', '1')
pymol.set('shininess', '10')
pymol.set('specular', '0.25')
pymol.set('ambient', '0')
pymol.set('direct', '0')
pymol.set('reflect', '1.5')
pymol.set('ray_shadow_decay_factor', '0.3')
pymol.set('ray_shadow_decay_range', '1')
pymol.unset('depth_cue')

pymol.color('black', 'elem C and ligand')
pymol.set('stick_color', 'white')

pymol.ray()

Finanlly, just say the image to wherever you like to store it. You could always try to change the above commands to meet your preference of a high quality image.

The general command pattern is pymol.do（‘the original pymol command you would put directly inside pymol’） pymol.fetch('PDB ID') pymol.set('object, number') pymol.show('surface')