Hi Peter, when i go to your site (http://www.chemeddl.org/resources/models360/models.php) i often receive this anwer from the applet: reader was not found: gaussian". Problably where molecular orbitals can be displayed. Is it a local problem ? It seems as if some javapllets are missing. Pino
Il 17/10/2011 23.26, David P. Pieper ha scritto: > I am working on the Chemical Education Digital Library project under > the supervision of Professor John Moore. Over the course of several > years, Xavier Prat-Resina worked as a postdoc to develop a tool called > "Models 360". It makes extensive use of Jmol to allow users to > investigate a collection of 3-D interactive models of organic and > inorganic compounds. The program was developed using version 11.8.12 > of Jmol and works as expected with this version. Some time ago we > decided it would be best to update the program to use a newer version > of Jmol. Originally we attempted to use 12.0.15, and we experienced > issues. Ownership of ChemEd DL is being transferred from the > University of Wisconsin - Madison to the American Chemical Society, > and prior to the complete transfer we would like to revisit the idea > of implementing a newer version of Jmol (likely 12.2.0). The issues we > experienced were encountered when we tried to view Molecular > Electrostatic Potentials using the program. The live Models 360 > program working (with version 11.8.12 of Jmol) can be viewed here > http://www.chemeddl.org/resources/models360/ > > > If we try to use our MEP options with version 12.2.0 of Jmol, some > will fail. Specifically these are the results (I took messages from > the Java Console): > MEP on Isopotential Surface: Seems to work, appears to render slightly > differently than in 11.8.12 > MEP on van der Waals Surface (Scale vdW volume 100.0%): script ERROR: > decimal number out of range (0.0 - 16.0)---- isosurface pos01> > > 100.0< < % resolution 6 solvent mep > MEP on a Plane (0 0 2 -1.0): pos01 created with cutoff =NaN min=0.0 > max=0.0; isosurface count: 0 (this also seems to freeze Jmol, with a > page refresh required) > This will happen with the XY, XZ, or YZ options checked when you press > "Set plane equation" > > You can see this for yourself at this development version I'm using: > http://144.92.39.69/dev/resources/models360/ > > We are using an extensive Javascript file to pass instructions and > variables to Jmol. > (http://144.92.39.69/dev/resources/models360/library/jmolfunctions.js > ). I'm assuming there are differences between versions involving how > Jmol expects to receive commands/variables/options (a number rather > than text or a range of acceptable values) for these MEP options. I > would guess the functions in question are > "setmepoptions(sign,appletid)" or "get_mep_cutoff(appletid)". > Otherwise, there might be a syntax error that the older version of > Jmol let slip by. > > Interestingly enough, while in 11.8.12 the "MEP on a Plane" option > appears to work, the console displays something such as the following: > pos01 created with cutoff = 0.0 ; number of isosurfaces = 1 > color range -0.05 0.05; mapped data range 0.031795057 to 0.8016224 > script ERROR: number expected > ---- > color isosurface absolute -0.1> > +< < 0.1000 > script ERROR: number expected > ---- > color isosurface absolute -0.1> > +< < 0.1000 > > > Not having extensive knowledge of chemistry or Jmol myself, my hope is > that someone from this list will be better able to decipher the errors > and at least point me in the right direction. If I have a better idea > of what Jmol is expecting, I might be able to find the portion in our > Javascript code that is passing an improper command to Jmol. I assume > the newer version of Jmol still supports these functions in some shape > or form. Let me know if I can offer any additional information or > insight about the resource so that other users could more easily help > me out. > > > Thank You, > David Pieper > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2d-oct > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
