User:Eric Martz/Sandbox 8: Difference between revisions
Jump to navigation
Jump to search
Chemistry of Water and Its Hydrogen Bonds
One Molecule
Technical Information
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| (4 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Chemistry of Water and Its Hydrogen Bonds== | |||
Prepared in collaboration with [[User:Gabriel Pons]]. | |||
===One Molecule=== | |||
<applet size='400' frame='true' align='right' caption='Insert caption here' | <applet size='400' frame='true' align='right' caption='Insert caption here' | ||
scene='User:Eric_Martz/Sandbox_8/Water/2' /> | scene='User:Eric_Martz/Sandbox_8/Water/2' /> | ||
*(<scene name='User:Eric_Martz/Sandbox_8/Water/2'>restore initial scene</scene>) | *(<scene name='User:Eric_Martz/Sandbox_8/Water/2'>restore initial scene</scene>) | ||
*<scene name='User:Eric_Martz/Sandbox_8/Water/4'>partial charge values</scene> | *<scene name='User:Eric_Martz/Sandbox_8/Water/4'>partial charge values</scene> | ||
*<scene name='User:Eric_Martz/Sandbox_8/Water/6'>shape of the molecule (spacefilling)</scene> (van der Waals radii) | *<scene name='User:Eric_Martz/Sandbox_8/Water/6'>shape of the molecule (spacefilling)</scene> (van der Waals radii) | ||
| Line 9: | Line 12: | ||
---- | ---- | ||
===Technical Information=== | |||
The following scene demonstrates a problem with greek letters in labels in Jmol | |||
*<scene name='User:Eric_Martz/Sandbox_8/Water/3'>partial charges</scene> (using δ in the label, it gets corrupted) | |||
Script for translucent MEP colored surface: | Script for translucent MEP colored surface: | ||
<pre> | <pre> | ||
Latest revision as of 00:12, 22 September 2010
Chemistry of Water and Its Hydrogen BondsChemistry of Water and Its Hydrogen Bonds
Prepared in collaboration with User:Gabriel Pons.
One MoleculeOne Molecule
|
- ()
- (van der Waals radii)
- Positive (+), Negative (-)
Technical InformationTechnical 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