[Jmol-users] Script pending slow to execute jmolMenu problem in MSIE
Experimenting with version 10.x.38b and FireFox 1.5.0.6 on Win-XP I find that the command script MyScript.txt might execute immediately or might hang for many seconds. This whether it is executed from a script on load, from a jmolMenu list or from the Console. In the latter case the Console writes pending while waiting, but then executes the script some seconds later with no error message. This even with a very simple script. Other commands within jmolMenu execute immediately. A separate problem is that jmolMenu does not give a menu list with MSIE 6.0.2900.2180.xpsp... It just writes out the menu items as text. The same jmolMenu works fine with FireFox. I am now trying (unrelated) to use picking to switch on/off bonding/polyhedra for elements selected by clicking. That should be possible, but I haven't yet succeeded :-) Alan. PS, I now have animated polyhedra with multiple CIF frames working fine on: http://icsd.ill.fr/icsd/help/CIF-help.html _ Dr Alan Hewat, ILL Grenoble, FRANCE[EMAIL PROTECTED]fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm _ - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Mac Safari Question
I have updated my machine to a iMacIntel. I am running 10.4.7, thus far without the latest security update. While I am pretty sure things were working with jmol yesterday, today I find that safari will not load the jmol aplet. I get a _javascript_ error; but I am pretty sure it is because the applet did not load so that it is not seen to load a molecular structure into it. In fact, the java console never opens, indicating to me that it is not recognizing the call for the applet. I have looked at the page successfully using a G4 with safari (10.4.5). It runs fine on the intel mac using any of the mozilla browsers or shiira. Omniweb and Opera still do not like it.Any one with a clue; is this an intel issue, or more likely, a 10.4.7 issue?Phil BaysJ. Philip BaysDepartment of Chemistry and PhysicsSaint Mary's CollegeNotre Dame IN 46556[EMAIL PROTECTED] - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] messaging arbitrary signal strings
I am beginning to try to use messageCallback for FirstGlance in Jmol. It appears to me that Jmol 10.2.00 does not message comments, even with set debugscript on. In the past (Protein Explorer) I have extensively used comments messaged by Chime to detect where Chime is in executing a command script. Can someone tell me how I can message an arbitrary signal string in Jmol? If not, I would like to request a new command message that would simply message whatever follows after the word message, e.g. message this arbitrary signal text Alternatively, comments could be messaged with set debugscript on. However, this seems less desirable since one then needs three commands to insert a marker string into the message stream: set debugscript on # arbitrary signal string set debugscript off (but in Jmol 10.2.00, # arbitrary signal string is not messaged.) As a temporary workaround for messaging an arbitrary string, I am using this scheme: set debugscript on define arbitrary_signal_1 none set debugscript off Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] messaging arbitrary signal strings
I am beginning to try to use messageCallback for FirstGlance in Jmol. It appears to me that Jmol 10.2.00 does not message comments, even with set debugscript on. In the past (Protein Explorer) I have extensively used comments messaged by Chime to detect where Chime is in executing a command script. Can someone tell me how I can message an arbitrary signal string in Jmol? If not, I would like to request a new command message that would simply message whatever follows after the word message, e.g. message this arbitrary signal text Alternatively, comments could be messaged with set debugscript on. However, this seems less desirable since one then needs three commands to insert a marker string into the message stream: set debugscript on # arbitrary signal string set debugscript off (but in Jmol 10.2.00, # arbitrary signal string is not messaged.) As a temporary workaround for messaging an arbitrary string, I am using this scheme: set debugscript on define arbitrary_signal_1 none set debugscript off Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Release notes for Jmol 10.3 or 11?
I see that Jmol prerelease 10.3.1 is available for download. Can someone give me the URL for the notes about what the changes are in 10.3 and 10.3.1? Ditto for Jmol 11 (and where is the download?)? Thanks, -Eric - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac Safari Question
On Aug 9, 2006, at 12:55 PM, Philip Bays wrote: I have updated my machine to a iMacIntel. I am running 10.4.7, thus far without the latest security update. While I am pretty sure things were working with jmol yesterday, today I find that safari will not load the jmol aplet. I get a javascript error; but I am pretty sure it is because the applet did not load so that it is not seen to load a molecular structure into it. In fact, the java console never opens, indicating to me that it is not recognizing the call for the applet. I have looked at the page successfully using a G4 with safari (10.4.5). It runs fine on the intel mac using any of the mozilla browsers or shiira. Omniweb and Opera still do not like it. Any one with a clue; is this an intel issue, or more likely, a 10.4.7 issue? I am running 10.4.7 on a MacBook, and I can load Jmol in Safari without trouble (from http://jmol.sourceforge.net/). it sounds like a site issue; can you provide a url to test that does not work for you? regards, tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. grasp. learn. ph: 919-368-2667 http://www.molvisions.com/im: molvisions usa:virginia:blacksburg tx: [EMAIL PROTECTED] Anyone who considers arithmetical methods of producing random digits is, of course, in a state of sin. - J von Neumann - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
