Home > PyMOL > Hydrogen bond
Display of Hydrogen bond
Display of Hydrogen bond is simple.
Action → find → polar contacts → select from menu
Helix is shown in the figure below. (I selected "without solvent".)
Example -Protein-Ligand interface-
I'll show you how to display hydrogen bond between protein and ligand.
I use RNase and 3'GMP complex.
- Selection of ligand
select gmp, resn 3gp
- Display of hydrogen bond
panel of ligand that created
Action → find → polar contacts → to other atom in object
Hide → everything
Show → stick
Show → cartoon
Display of water molecule as sphere model ...
show sphere, resn hoh
set sphere_scale, 0.2
Deletion of water molecule ...
1.click to select water molecule
2.(all)Hide → Sphere
3.(sele) Show → Sphere
Turning of main chain ...
set cartoon_side_chain_helper, on
Example -Protein-Protein interface-
I'll show you how to display hydrogen bond between protein and Protein.
I use Nectin-1 homodimer.
- Selection of molecule
Select chainA
select molA, chain A
- Display of hydrogen bond
panel of chainA that created
Action → find → polar contacts → to other atom in object
See also Interaction interface.