User:Eric Martz/Sandbox 8: Difference between revisions
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<applet size=' | ==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' | |||
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) | ||
*<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> | ||
---- | |||
===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> | |||