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