To visualize hydrogen bonds in Pymol between a protein and the surrounding water molecules, I tried using "Action -> Find -> Polar Contacts -> Involving solvents", which shows hydrogen bonding between solvent molecules and protein and hydrogen bonding between different solvent molecules, making visualizing hbonds between just the solvent and protein very messy. Is there a way (that preferably does not involve writing a script) to display only the hydrogen bonding between the solvent and protein?
I encounter a similar problem in VMD, where I tried to create an HBond representation with the selected atoms as "protein or (water and within 3 of protein)"
In Pymol, the appropriate command would be
show_contacts sel1, sel2, result="contacts", cutoff=3.6, bigcutoff=4.0
https://pymolwiki.org/index.php/Show_contacts for link to the appropriate plugin
with sel1 replaced by "polymer" and sel2 by "solvent"
I successfully found hydrogen bonds and visualized them using https://pymolwiki.org/index.php/Show_contacts thanks to Annemarie Honegger
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