User:Eric Martz/Sandbox 8: Difference between revisions
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Chemistry of Water and Its Hydrogen Bonds
One Molecule
Technical Information
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==Chemistry of Water and Its Hydrogen Bonds== | ==Chemistry of Water and Its Hydrogen Bonds== | ||
Prepared in collaboration with [[User:Gabriel Pons]]. | 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' /> | ||
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*<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) | ||
*<scene name='User:Eric_Martz/Sandbox_8/Water/5'>translucent surface colored by molecular electrostatic potential</scene> <font color="blue"><b>Positive (+)</b></font>, <font color="red"><b>Negative (-)</b></font> | *<scene name='User:Eric_Martz/Sandbox_8/Water/5'>translucent surface colored by molecular electrostatic potential</scene> <font color="blue"><b>Positive (+)</b></font>, <font color="red"><b>Negative (-)</b></font> | ||
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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