(John, there's a note for you, below) Alan Hewat wrote:
>With lots of help from Bob Hanson and his version 10.x.20, I now have an >automatic Jmol display of ICSD database inorganic structures, complete with >co-ordination polyhedrae eg see: >http://icsd.ill.fr/icsd/index.php?action=Search&elements=cu+o&elementc=3 >After clicking Demo in the login box, click on each Struct.Formula. Thanks >Bob. But I have a couple of new questions :-) > > > This is just TOO cool! And, Alan, I fixed the square planar and problem. Look for the fix in 10.x.20a >1) How can I display the structure formula along with the cell data in the >Java window? > > Do you have the exact formula already, or do you need to calculate it? If you already have it, you can use "echo" -- see examples at http://www.stolaf.edu/people/hansonr/jmol/docs If you want Jmol to extract it from the CIF file, I've added three new fields to the auxiliaryInfo for CIF files: auxiliaryInfo.models[0].structuralFormula="Cu (Ge O3)" auxiliaryInfo.models[0].formula="Cu1 Ge1 O3" auxiliaryInfo.models[0].chemicalName=" Copper germanate" There are a few ways you can access these with JavaScript. Not much documentation on this. But basiscally you could use: var chemName = jmolGetPropertyAsArray("auxiliaryinfo").models[0].chemicalName To see the whole list, use the script command getProperty "auxiliaryInfo" There's a bunch of symmetry-related stuff there you might like to see. Do this at the test/proto site to see what it gives in the textbox. >2) Can I do animation (flipping between two or more CIF structures) or is this >just for PDB ? > > If your cif file contains more than one data block, then each data block will be loaded separately into its own "frame" or "model" -- model 1, model 2, etc. If you want a specific model from a multi-model CIF file, use load "myfile.cif" n where "n" is the model number. This can be used along with {i j k}: load "myfile.cif" 3 {2 2 2} >3) Can I display a "slab" of a CIF structure, or is this just for PDB ? > > slab is for anything. Also depth. See that documentation. >(Eventually I would like to have two slider controls on my web page - one to >set the slab percent depth and one to move the slab through the structure to >explore it, and some way of orienting it). > > sliders are no problem. I developed a simple slider package for another project; perhaps others are around. John Gelder is in the process of setting up a page that uses sliders to control dipole lengths and other properties. John, can you share that URL with us and tell us about how you got those sliders going? >4) Can the user export the contents of the Applet window to jpeg or Povray, or >is this only for the Jmol application ? > > > just the application. The applet doesn't have access to the needed functionality. Povray is only very minimally supported, you might have noticed, but I'm trying to organize a team to develop Povray more, particularly with isosurfaces and biomolecular structure. It really shouldn't be that hard -- the "renderers" are very simple and could fork to a different set of functions in the case of Povray output, I think. Bob Hanson >Alan. >_____________________________________________________________ >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=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > 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=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
