OK, I've got it. A good use for -0.0 (which is NOT exactly the same in
Java as 0.0)
On Sat, May 12, 2012 at 10:22 PM, Robert Hanson wrote:
> how interesting! Yes, that makes sense. The only way I can think of to fix
> this is to set one of the partial charges to a very small number -- 1E-10
> -
how interesting! Yes, that makes sense. The only way I can think of to fix
this is to set one of the partial charges to a very small number -- 1E-10
-- so that it triggers Jmol to consider partial charges as having been set.
Any objection to that?
Bob
On Fri, May 11, 2012 at 9:47 AM, Pillot Paul
Congratulations, Bob! what a wonderful addition!
Frieda
On May 7, 2012, at 6:52 PM, Robert Hanson wrote:
> Jmol 12.3.24 will calculate charges using the MMFF94 model. Thus, you will be
> able to do this:
>
> load caffeine.xyz
> calculate partialcharge
> isosurface vdw map mep
>
> It was an int
Thank you Paul. Your approach is certainly cleaner. If you're wondering what
var z="" is all about, I don't have a clue. It's obviously a remnant of a lot
of trial an error fumbling around to find out why the zero charges were not
being mapped.
Otis
--
Otis Rothenberger
o...@chemagic.com
http:
Thanks Otis !
I've just tried this trick by setting "{*}.partialcharge = 0.1;
{*}.partialcharge=0.0" and it works (apparently there is no need to loop
through all the atoms).
I solved my problem by just doing a simple check after "calculate
partialCharge" and before isosurface creation :
if ({*
Paul,
This is one of those problems that I know how to fix, but I don't know why the
fix works. For the PubChem alkanes (or any PubChem all zero atom charged
molecules), here's how I fixed the problem:
if
(jmolGetPropertyAsString("stateInfo").indexOf("PUBCHEM_MMFF94_PARTIAL_CHARGES")
> -1) {
Otis,
I think the green surface is great and I was just wondering how it could be
displayed for alkanes. My guess is that it's not displayed because when there
is no partial charge, no MEP surface can be created. The problem is "how does
Jmol guess there is no partial charge in the file?", and t
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