From: SourceForge.net <no...@so...> - 2011-01-22 14:37:48
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Bugs item #3156530, was opened at 2011-01-12 20:00 Message generated for change (Comment added) made by nobody You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3156530&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Applet Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Bob Hanson (hansonr) Summary: isosurface display Initial Comment: Hello, I'm having problems displaying the homo and lumo from .cube files on the JMol applet. I have links below the applet that updates the displayed molecule so that the homo or lumo can be shown. Sometimes it works correctly. Other times only the positive or negative surface is displayed. Sometimes no surface is displayed. I am attaching screenshots of all three cases from the same molecule. I am also attaching a cube file that I use to get the isosurface info for the homo. Here is what the script looks like that updates the display of the molecule: <script type="text/javascript"> jmolInitialize("${jmol_url}"); jmolApplet(700, "load ${homo_cube_url}"); jmolSetLinkCssClass("jmol-link"); jmolBr(); jmolLink("isosurface off", "Clear"); jmolLink("isosurface off; isosurface pos color red cutoff ${doc.results.homo_contour} ${homo_cube_url}; isosurface neg color blue cutoff -${doc.results.homo_conto ur} ${homo_cube_url}", "HOMO"); jmolLink("isosurface off; isosurface pos color red cutoff ${doc.results.lumo_contour} ${lumo_cube_url}; isosurface neg color blue cutoff -${doc.results.lumo_conto ur} ${lumo_cube_url}", "LUMO"); </script> Craig ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2011-01-22 14:37 Message: Here is the out put after the following happened: 1. I clicked the "HOMO" link and the homo surface displayed correctly. (see the script in my original bug submission) 2. I clicked the "LUMO" link and nothing appeared except the molecule. 3. I clicked the "LUMO" link again and nothing appeared except the molecule. 4. I clicked the "LUMO" link once again and the isosurface displayed correctly. isosurface1 created with cutoff=0.025 min=-0.15647899 max=0.16178499; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 isosurface1 created with cutoff=0.025 min=-0.15647899 max=0.16178499; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 isosurface1 created with cutoff=0.025 min=-0.15647899 max=0.16178499; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 isosurface1 created with cutoff=0.023 min=-0.180083 max=0.190436; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-01-20 19:34 Message: We need to see that Java (not the Jmol) console output after one of the failures. From the Jmol script console, enter: set debug Then see if you can get it to fail. Copy the entire contents of the Java console. If you need to send this to me off-list, send that to me at ha...@st... ---------------------------------------------------------------------- Comment By: Jonathan Gutow (gutow) Date: 2011-01-20 18:22 Message: I have an idea from my experience running Jmol as the 3-D viewer in the SAGE math web interface. This sounds like a timing issue related to AJAX type calls. Are there requirements for updates from your server related to this? The code you are using does not seem to imply this, but intermittent behavior is what I saw when I didn't set things up to make sure the server or the applet was ready to respond to a request. Just and idea. ---------------------------------------------------------------------- Comment By: https://www.google.com/accounts () Date: 2011-01-20 16:56 Message: When the error happens, the console shows the exact same output as when the surface is correctly displayed. I don't think it is the cutoffs, because, in answer to your 'Third' point, the randomness happens like this. I go to a record for one of our molecules and and hit the HOMO link. That link may or may not cause the surface to correctly display. If I click the same exact link again, once again, the surface will display or not. In all cases the console shows the same exact output. I wish I could point you to a web site, but this is internal to our organization. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-01-14 21:02 Message: First, if you can figure out how to open the Java console (not the Jmol console) you might find some sort of error there. Second -- could be the cutoffs. Third -- the randomness of this makes no sense. Not sure you mean sometimes with one molecule, sometimes with another, or sometimes with the same orbital and sometimes not, but with the same orbital. I can't imagine what is going on there, unless it's something about memory -- that you are not selecting out the specific subset of atoms or something. If you could point me to the web site, that might be best. ---------------------------------------------------------------------- Comment By: https://www.google.com/accounts () Date: 2011-01-14 15:48 Message: Thanks for pointing out the SIGN keyword. After switching to: jmolLink("isosurface off; isosurface SIGN color red blue cutoff ${doc.results.homo_contour} ${homo_cube_url}", "HOMO"); The behavior changed. Now I never get just a positive or negative surface, instead it is sometimes displayed correctly, or not at all. Just a rough estimate, but hitting the HOMO link gives me about a 1 in 3 chance of seeing the isosurface. When I watch the console, it will indicate that an isosurface was created even when it does not appear on the molecule: isosurface1 created with cutoff=0.017 min=-0.116008 max=0.11920901; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-01-12 23:54 Message: No need to use two surfaces -- just use the SIGN keyword. This applies your cutoff to both positive and negative cutoffs and gives you surfaces for both: isosurface SIGN yellow green cutoff 0.01 data/benzene-homo.cub.gz ---------------------------------------------------------------------- Comment By: https://www.google.com/accounts () Date: 2011-01-12 20:03 Message: Oops. I didn't get the other files attached that I meant to. I'm not sure how to upload the images that show the surface incorrectly displayed. If anyone needs them please let me know how to get them attached. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3156530&group_id=23629 |