Demonstrating Polar Interactions Between a Protein and a Ligand in PyMOL

Showing Polar Interactions

1. Select the ligand in the model and rename the object to 'ligand'.
2. Select the ligand, then choose actions->around->residues within 5 angstrom. Rename the selected object to 'active' and show the residues as sticks.
3. Find the polar contacts: action->find->polar contacts->to other atoms in object.
4. Dashed lines may connect to blank areas, which may be caused by hidden water. Display water molecules within 3.2 angstroms (hydrogen bonds are shorter than 3.2 angstroms) with select $LigandWater, (($ligand)around 3.2) and(resn HOH); an object named '$LigandWater' will be created.

Export

1. Click the middle mouse button on an atom to center the view on it, then rotate to a suitable angle to show the interaction.
2. Set the background to white: Display->background->white.
3. Click Draw/Ray, set it to 300 DPI, and click Ray.
4. Optionally remove shadows: setting->Rendering->shadows->None.

References

1. https://www.bilibili.com/video/BV1rf4y1v7hL/