It depends upon which type of surface is generated -- sasurface and solvent
specifically do ignore water. The others (vdw, moleular) do not. I'll note
that.
Just use "solvent" instead of "molecular" -- no need to change files!
Not planning to change any defaults.
On Sat, Sep 18, 2010 at 11:27 AM, Eric Martz
<[email protected]>wrote:It de
>
> 2. I want to color the surface by MEP. It appeared that I had no problems
> setting the partial charges with
>
> {hydrogen}.partialCharge = 0.41
> #{oxygen}.partialCharge = -0.82
> {nitrogen}.partialCharge = -0.82
>
> The documentation says that
>
> isosurface resolution 6 solvent map mep
>
> will use the partialCharge atom properties. It did not (surface was all
> blue). Is this a bug or a problem in the documentation?
>
>
should work -- works for me...
Check the data range, which is reported when you do the default mapping. The
default for MEP is just -0.1 to 0.1. Your values are probably all > 1.
isosurface vdw map color range -1 1 mep
for examples.
> 3. The MEP section of the isosurface documentation says that "if MEP is
> followed by PROPERTY xxxx" it will be used instead of partial charges.
> However,
>
> isosurface resolution 6 solvent map MEP property partialcharge
>
> produced an all-blue surface. Is this a bug?
>
>
just that range problem -- you haven't set a decent range.
> 4. In order to color the surface, I omitted "MEP":
>
> isosurface resolution 6 solvent map property partialcharge
>
> This produced the default yellow-green-blue surface. But I want a
> red-white-blue surface as is conventional for MEP. OK, so this worked
>
>
right - but it's not a MEP. Just charges.
you need also before MEP or PROPERTY:
colorscheme "rwb"
or
colorscheme "bwr"
or after the isosurface command, you need
color isosurface "bwr"
or
color isosurface "bwr" range 5.0 10.0
or such.
> isosurface resolution 6 solvent map MEP property partialcharge colorscheme
> "rwb"
>
> except that the "red" was pink and the "blue" was deep blue, despite the
> isosurface report claiming "isosurface full data range -0.82 to 0.41 with
> color scheme spanning -0.82 to 0.41".
>
>
must have been a trace of red in there somewhere.
> I tried a few things to get a redder color at the reddest end of the
> colorscheme, without success.
>
> Is there some way I can get the "red" in the "rwb" color scheme to be
> redder (more saturated)?
>
>
just change your color scheme range to something like -0.5 to 0.41
Bob
> Thanks! -Eric
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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