User:Eric Martz/Sandbox 8

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Revision as of 19:18, 19 September 2010 by Eric Martz (Talk | contribs)
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Insert caption here

Drag the structure with the mouse to rotate
  • ()
  • (using δ in the label, it gets corrupted)
  • (van der Waals radii)
  • Positive (+), Negative (-)

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

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Eric Martz

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