User:Eric Martz/Sandbox 8
From Proteopedia
Chemistry of Water and Its Hydrogen Bonds
Prepared in collaboration with User:Gabriel Pons.
One Molecule
|
- ()
- (van der Waals radii)
- Positive (+), Negative (-)
Technical Information
The following scene demonstrates a problem with greek letters in labels in Jmol
- (using δ in the label, it gets corrupted)
Script for translucent MEP colored surface:
{hydrogen}.partialCharge = 0.41 {oxygen}.partialCharge = -0.82 # IMPORTANT: the SOLVENT version of isosurface # IGNORES WATER UNCONDITIONALLY! We must us MOLECULAR! #isosurface resolution 6 MOLECULAR colorscheme "rwb" map MEP isosurface resolution 6 MOLECULAR map MEP # Higher values of resolution make a choppier surface that rotates # more jerkily. 6 is good. color isosurface "rwb" range -0.2 0.2 # chose this range by trial and error. # default is -0.1 0.1 as reported by the isosurface command. color isosurface translucent 2 # or the partial charges could be in the PDB file using # this command to transfer the values. # {*}.partialCharge = {*}.temperature.all
Possible script for large translucent hbonds:
select all calculate hbonds hbonds 0.3 color hbonds white color hbonds translucent 6