Actually, it doesn't matter much how the color range is determined though
confounding. If there is a method, it should be able to invoked, is it?
>>> using cmd : show isosurface
I am a able to get the default parameters for the color range setting, but
it doesn't really solve my question since the isosurface1(the parameters) is
only calculated once the menu "electrostatic surface" is called. What I
want is to replace menu click.
_________________________________
Wenhan Chen
School of Chemistry and Molecular Biosciences
The University of Queensland
2013/5/20 Otis Rothenberger <[email protected]>
> Exactly! I'm confused. I recall trying to make some sense of this in the
> Spartan docs, but I never found a clear answer. In Jmol, I believe that the
> range is intended as a charge mim/max set, but there is a definite lack of
> magnitude consistency in say Spartan vs MMFF94 or Accelrys charges.
>
> The -.07 .07 range is a pure trial and error range. I don't have a clue
> what units are involved here. This is a long standing question for me. Does
> anyone know?
>
> Consider 1-butanol oxygen:
>
> Spartan -0.738399
> MMFF94 -0.6800
> Accelrys -0.3962
>
> I understand that different algorithms are used resulting in different
> charges based on different assumptions, but in some cases I see power of
> ten differences. Color me unit confused.
>
> Otis
>
> --
> Otis Rothenberger
> [email protected]
> http://chemagic.com
>
>
>
>
> On May 19, 2013, at 1:09 PM, Pshemak Maslak wrote:
>
> On 5/19/2013 12:25 PM, Otis Rothenberger wrote:
>
> Chen,
>
> The menu command is:
>
> isosurface delete resolution 0 molecular map MEP translucent
>
> This hides an important issue that I don't fully understand because of
> seemingly inconsistent charge units in various files. The issue is the
> charge range of painted colors. The above uses a default range that I don't
> know. Angel, do you know the default? By trial and error, I settled on the
> following:
>
> isosurface resolution 0 molecular color range -.07 .07 map
> mep translucent
>
>
> Otis
>
>
> BTW: what are the units for MEP? What is " -0.07" in the example above?
> Is that number for potential energy? Or just Q/distance? (Q in what
> units, distance in what units)? Or something else?
>
> PM
>
>
>
>
>
>
>
> --
> Otis Rothenberger
> [email protected]
> http://chemagic.com
>
>
> On May 19, 2013, at 11:49 AM, Angel Herráez wrote:
>
> Hello Chen
>
> You can try enetering this in the script console just after you use the
> menu option:
>
> show isosurface
>
> amongst the long text displayed, there is a section entitled
> <jvxlIsosurfaceState>
> which has the script that will render the isosurface you have.
>
> As for getting a color, you can include the color definition in your
> isosurface script, but sometimes that is a little tricky, and it is always
> safe and easy to apply color in a second command, like e.g.
>
> isosurface mysurf1 molecular;
> color $mysurf1 translucent* * green;
>
>
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