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== | |||
Prepared in collaboration with [[User:Gabriel Pons]]. | |||
<scene name='User:Eric_Martz/Sandbox_8/ | ===One Molecule=== | ||
<applet size='400' frame='true' align='right' caption='Insert caption here' | |||
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/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/5'>translucent surface colored by molecular electrostatic potential</scene> <font color="blue"><b>Positive (+)</b></font>, <font color="red"><b>Negative (-)</b></font> | |||
---- | |||
===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: | |||
<pre> | |||
{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 | |||
</pre> | |||
Possible script for large translucent hbonds: | |||
<pre> | |||
select all | |||
calculate hbonds | |||
hbonds 0.3 | |||
color hbonds white | |||
color hbonds translucent 6 | |||
</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