On Sat, Jan 23, 2010 at 9:33 PM, Grossman, Robert B <[email protected]
> wrote:
> We can let Jmol create the MO from the QM data in the browser - I think
> that is what we are doing now with the .mo file - but we greatly prefer to
> read the QM data from the database, not from a file.
>
> I'm still trying to understand the mutual dependencies among load,
> isosurface, and mo.
>
> When I use "jmolLoadInline()" with the contents of the .mo file, I can see
> the structure, and I can use the script "mo" (as implemented by the
> jmolMenu() JS command) to display the MOs.
>
>
By .MO file, not sure what you mean there, unless that's a WebMO file. The
fact that you can use the MO command indicates that you are creating the
orbitals from the basis functions and coefficients.
> When I use "jmolLoadInline()" with the contents of the .jvxl file, I can
> see the structure, but I cannot find a script that will display the
> isosurface. Is there a script that will display the isosurface after I load
> it into Jmol with "jmolLoadInline()"?
>
>
>
This older JVXL file format was modeled on the CUBE format and thus did save
up to the first 100 atoms; the newer XML version doesn't. But all you are
doing there is reading the atoms. The load command doesn't read any surfaces
ever. If the file has QM basis and coefficients, then those are read at load
time (and the popup menu will be populated with items showing all the
orbitals and their energies).
The JVXL file is really a surface file and is read using the ISOSURFACE
command. Until last week you couldn't load those inline. (You could load
PMESH data -- simple triangles -- inline, but you couldn't use the
isosurface INLINE keyword with anything else. I think I changed that early
last week. So if that's really what you want to do, you need to use Jmol
11.9.21.
So you can load MO data two ways -- with the LOAD/MO command combination or
with the ISOSURFACE command. In Jmol "MO" is a subset of "ISOSURFACE" so the
same code is run, but the options are a bit different. When you use
MO homo
you get a basic, standard orbital, with a nice listing of orbital properties
in the upper left corner. Options are pretty much limited to cutoff and
color. With
ISOSURFACE MO homo
you don't get that listing, but you have a bit more flexibility -- you can,
for example, choose to ignore atoms and only see contributions from a
subset, and you can do contouring, planar slices, "topo" maps, and such. I
need to get this into the documentation....
Bob
>
> On 1/23/10 8:39 PM, "Robert Hanson" <[email protected]> wrote:
>
> I think it just got mangled as being part of the email.
>
> isosurface is used to create MOs from files that are not QM files. --
> surfaces.
> mo is used to generate the MO data directly from the basis functions. Most
> people these days, I think, just let Jmol read the QM file and create the MO
> in the browser -- no need for a server end. Are you certain you can't do
> that?
>
> Bob
>
> On Sat, Jan 23, 2010 at 6:08 PM, Grossman, Robert B <
> [email protected]> wrote:
> Hi Bob,
>
> The information is read from an Oracle database and written into a JSP
> page. We have the ability to write information to files, but we want very
> much to avoid having to do it. We also want to avoid having to deal with
> multiple files to display a single molecule and its associated MOs. From my
> point of view, Jmol's preference for loading information from files is a
> real drawback.
>
> We worked around the problem by using a .mo file instead of a .jvxl file.
> We were able to load the .mo file inline and display its MOs without any
> problem. A friend gave us the proper Jmol JS commands to use to display the
> MOs. jmolMenu([['mo delete;','none'],['mo 3',"3"],['mo 4',"4"] ...]); . No
> "isosurface" commands.
>
> I don't think that we could have mangled the .jvxl information because the
> .mo information, which was loaded and transmitted in exactly the same way,
> was not mangled. But I could be wrong.
>
> So is it correct that we use "isosurface" to load MOs into Jmol, and we use
> "mo" to induce Jmol to display them?
>
> -- Bob
>
> On 1/23/10 5:44 PM, "Robert Hanson" <[email protected]> wrote:
>
> Well, two things. First, you must have mangled the data some way - or at
> least clipping from this page doesn't work. Because the attached file did
> run. Second, you can only load an isosurface "inline" like that in the very
> latest version of Jmol. (I'm not sure it's even in the one I have up at
> http://chemapps.stolaf.edu) What you would need to do is (all Jmol script
> here)
>
> isosurface INLINE @{javascript("getMol()")}
>
> that tells Jmol to read the output of the JavaScript getMol() function as
> the data for the isosurface instead of reading the data from a file.
>
> Any reason you don't want to have that data in a file? -- or is this coming
> back from a server and you are trying to keep it all together? Sure would be
> simpler:
>
> isosurface "somefile.jvxl"
>
> Bob
>
>
>
> On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B <
> [email protected]> wrote:
> Hi,
>
> I have a JVXL file containing MO data that I am trying to display. I can
> see the molecule, but I can't see the MO. I have tried various scripts to
> turn on the MO, to no avail. Below I have copied the relevant part of my
> Web page. I am using 'mo HOMO;' as the script, but I have tried several
> other commands, including none, to no avail. How do I display the MO? Does
> the fact that I load inline prevent the MO from being displayed?
>
> -- Bob
>
> <script type="text/javascript">
> // <!--
> function getMol() {
> return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15
> 2008-11-24 13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028,
> -4.170638, -6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type:
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> [email protected]
> 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
------------------------------------------------------------------------------
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
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
