Re: [Jmol-users] iSpartan files and a question

[Robert Hanson]

Looks to me that you need to use a .sparchive file, not .spartan, if you
want orbitals. The charge business is fixed; if you want to use Mulliken
charges, that can be done with

LOAD ... filter "charge=mulliken"

I've also just added

LOAD ... filter "natcharge"

just for you, Otis. ;)

Bob



On Wed, Jul 26, 2017 at 10:05 PM, Otis Rothenberger 
wrote:

> Bob,
>
> I decided to pull the charges out of the iSpartan files using Jmol's
> javascript getPropertyAsString with fileContent after the spartan file is
> loaded. This allows me to provide users with the ability to 3-way "toggle"
> MULCHARGES, ESPCHARGES, and NATCHARGES without reload of the model. The
> student user at Bradley is using this to study partial charges, so the
> "toggle" is a nice feature for her.
>
> The difference between my old spartan files and these new spartan files,
> iSpartan AND files from the latest version of "big" Spartan in use at
> Bradley University, is the number of spaces after the "PROP" markers!!! I
> made the old and new files compatible by parsing the files with regular
> expression splits.
>
> My next question with all of this is about MO data. I see now that what
> iSpartan is doing is providing limited MO data - HOMO, LUMO, and a few
> other MO's close to HOMO and LUMO.
>
> Here's a link to the text version of the iSpartan file for ethylene:
>
> http://chemagic.org/ethylene.txt
>
> Is there any chance of pulling HOMO and LOMO surfaces out to this file
> once it's loaded in Jmol via the aforementioned approach I used for charge?
>
> While the student at Bradley got me started on this, it seems to me that
> iSpartan is a very nice low budget way to access spartan files that might
> be of interest to my secondary school low budget users.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org
>
> 
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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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Re: [Jmol-users] Jmol Tutorial Manual now online and accessible

[Robert Hanson]

 Absolutely fantastic, Jeff. It is really rewarding to see such extensive
effort involving Jmol to make it possible for students to better understand
biochemistry. Wow.

The only thing I might add is that one no longer needs Jmol.jar. You might
consider mentioning at the top that what you are suggesting can be done at
the RCSB site itself, by opening a console, and that any site with JSmol
such as https://chemapps.stolaf.edu/jmol/jsmol/simple.htm can load PDB
files simply by drag-dropping a PDB file into it.

Bob
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