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
