Reichsman Frieda wrote:
>Thanks Bob. If I understand correctly, this means that Jmol is
>calculating the surface MEP based on the values in the file, which do
>not represent absolute MEP but rather, are partial charges. And that
>means that when Jmol calculates the surface MEP for only part of the
>amino acid (the side chain), the absence of the 'backbone' atoms
>greatly influences the calculation of the potential over the side
>chain, yes? And so the absence of those atoms is creating the effect
>I'm seeing of diminishing the potential on the charged side chain, and
>magnifying it a bit on the uncharged side chain?
>
>
That could be.
>This leads to another question, would it be possible to show a partial
>surface? That is, 'build' the surface for the entire amino acid, but
>only display only the surface over the side chain. I imagine this
>would be a feature request, would it be feasible to do this?
>
>
>
I think you want
isosurface select {xxxx} molecular map select {*} mep
That is, when you run the mep, you want to indicate that for THAT part
of the calculation, you want all atoms selected. I hadn't realized
myself that two selects work here -- I suppose it could be useful. Or not.
Bob
>Frieda
>
>
>On Aug 5, 2008, at 12:11 PM, Bob Hanson wrote:
>
>
>
>> if you are mapping MEP data, remember that a MEP calculation is
>>being done that converts charge on atoms to potential at some distance
>>(on the surface) from a bunch of atoms, collectively. This value falls
>>off with distance. So that's probably why your numbers are low. They
>>aren't just charges, and really they are just approximations of
>>electron
>>potential, as well. If you want to map the charges themselves, you
>>will
>>need to use "map property partialcharge". But that will look somewhat
>>blotchy, I suspsect.
>>
>>I'm sure you have the color range/absolute business correct.
>>
>>
>
>
>
>
>>Bob
>>
>>
>>
>>>Am I misunderstanding what "color range/absolute x.xxx y.yyy" should
>>>be doing? Is there a way to get the coloring for "color range all"
>>>but
>>>only show the surface for the side chains?
>>>
>>>Frieda
>>>
>>>
>>>//////////////////////////////////////
>>>
>>>Frieda Reichsman, PhD
>>>Molecules in Motion
>>>Interactive Molecular Structures
>>>http://www.moleculesinmotion.com
>>>413-253-2405
>>>
>>>//////////////////////////////////////
>>>
>>>
>>>
>>>
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>>--
>>Robert M. Hanson
>>Professor of Chemistry
>>St. Olaf College
>>Northfield, MN
>>http://www.stolaf.edu/people/hansonr
>>
>>
>>If nature does not answer first what we want,
>>it is better to take what answer we get.
>>
>>-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>>
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>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Build the coolest Linux based applications with Moblin SDK & win great prizes
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