Dear Pymol Users!
I wonder to ask regarding the algorithm implemented in pymol for the
calculation of the hydrogen bonds between ligand and protein using
preset.ligand_cartoon demonstrating the interactions?
I've just compared predicted hydrogen bonds for the same complex that
I could observe with Chim*ra and found that there were differences:
pymol tends to predict more hydrogen bonds considering additional
interactions located on the longer distances. Are there some built-in
commands in pymol that would allow me to modulate geometrical criteria
(cut-offs?) for the hydrogen bonds search assuming that I am operating
with multi-model pdb (results of docking) using command:
preset.ligand_cartoon('my_pdb*',_self=cmd)
Many thanks in advance
Cheers
Enrico_______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
