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 <otis@chemagic.com> 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 <hansonr@stolaf.edu> 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 <otis@chemagic.com>
> 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
>
> _______________________________________________
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>



--
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
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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