How do I create Protein Ligand images I was wondering how I can create images showing the bonds and the residue codes involved in the bound Protein Ligand complex obtained after Molecular Docking as depicted in the image below.
Pymol, in either its commercial or open source edition, will be sufficient to make figures such as your examples. Pymol recognises &quot;polar contacts&quot; for the intermolecular interactions and has labels that can be used for residue codes.
It is also scriptable and is widely used.