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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