Re: [Jmol-users] MEP Display

[Robert H. <ha...@st...>]

I think it would be nice to get a decent set of defaults there. I'm sure I
just guessed.

On Sun, Jan 24, 2010 at 5:43 PM, Otis Rothenberger <ot...@ch...>wrote:

> Bob,
>
> Thanks, that explains it.
>
> Yes, that was JavaScript. I should have mentioned that.
>
> Given your explanation, I think I'm going to play around with reading
> partial charges prior to MEP display and then explicitly setting a
> specific range based on a JS decision. I'm not sure this is doable,
> but given all you've done with Jmol, it may be.
>
> Otis
>
> On Sun, Jan 24, 2010 at 5:55 PM, Robert Hanson <ha...@st...> wrote:
> > Otis,
> >
> > [Just to be clear -- those commands you list are being defined in
> > JavaScript, not Jmol script -- can't do that *exact* command in Jmol
> script,
> > right? no " + " .... there without the script() function or using
> something
> > like @colors where colors is a user-defined Jmol variable ]
> >
> > Yes, MEP. The documentation is in error (or was a minute ago, at least).
> The
> > range is usually "ALL" as a default, but It's set up as a default for MEP
> to
> > be the range -0.05 to +0.05. This ensures that comparisons between
> molecules
> > is by default possible and prevents something like hexane from looking
> like
> > a strong nucleophile.
> >
> > But the range is probably too tight for general work, and I recommend
> > experimenting with different ranges and then settling on one that suits
> you.
> > If you find a set that is a better default, we could consider that for
> Jmol
> > 12, which I think is probably on the horizon.
> >
> > Bob
> >
> >
> >
> > On Sun, Jan 24, 2010 at 11:46 AM, Otis Rothenberger <ot...@ch...>
> > wrote:
> >>
> >> Hello-
> >>
> >> 1) I thought "range all" was default, but there must be another
> >> default. What is the default range in the above script context?
> >>
> >> 2) I think my first line of script above comes close to the Jmol left
> >> click menu script of "isosurface delete resolution 0 molecular map MEP
> >> translucent." Indeed, the menu produces the same blue m-nitrophenol (o
> >> and p as well). What is the current recommendation for a MEP script?
> >>
> >> Otis
> >>
> >> --
> >> Otis Rothenberger
> >> http://chemagic.org
> >>
> >>
> >>
> ------------------------------------------------------------------------------
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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
> >
> >
> ------------------------------------------------------------------------------
> > Throughout its 18-year history, RSA Conference consistently attracts the
> > world's best and brightest in the field, creating opportunities for
> > Conference
> > attendees to learn about information security's most important issues
> > through
> > interactions with peers, luminaries and emerging and established
> companies.
> > http://p.sf.net/sfu/rsaconf-dev2dev
> >
> > _______________________________________________
> > Jmol-users mailing list
> > Jmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
>
>
>
> --
> Otis Rothenberger
> http://chemagic.org
>
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for
> Conference
> attendees to learn about information security's most important issues
> through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
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