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. 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()"? 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
