pymol tutorial how to show ligand interactions

Rigorously determining the location of lone pair electrons and proton coordinates from raw PDB files is a nontrival problem especially when arbitrary small molecule structures are present. As it stands, all of those things are guessed heuristically. Generally speaking, PyMOL does not have sufficient information to rigorously determine hydrogen bonds, since typical PDB file are ambiguous with respect to charge states, bonds, bond valences, and tautomers.

'Polar contacts' check geometry as well as distance. The 'polar contacts' mentioned above are probably better at finding hydrogen bonds than these scripts. pdb h_add prot1 h_add prot2 select don, ( elem n, o and ( neighbor hydro )) select acc, ( elem o or ( elem n and not ( neighbor hydro ))) dist HBA, ( prot1 and acc ),( prot2 and don ), 3.2 dist HBD, ( prot1 and don ),( prot2 and acc ), 3.2 delete don delete acc hide ( hydro ) hide labels, HBA hide labels, HBD # NOTE: that you could also use this approach between two # non-overlapping selections within a single object. # EXAMPLE 2 # Show hydrogen bonds between two proteins load prot1.

Pymol tutorial how to show ligand interactions