Preparing a Jmol View of the Molecule

Draw a molecule in ACD ChemSketch v12 Freeware as usual. Under the Tools menu, select Add Explicit Hydrogens. Again under Tools, select 3D Structure Optimization. When the dialog box appears asking whether to Remove hydrogens before starting optimization, answer No. Under the File menu, select Save As and select the MDL Extended Molfile format. Answer OK when prompted that the selected format cannot be reopened and OK that some graphic features will be lost. The filename you enter should be MA####.mol, where the #### is replaced with the matrix ID number. Now you need to create an html file that opens the newly created .mol file in the Jmol applet. Copy the JMOLtemplate.htm template file (located in the file downloads section below) and rename it for the molecule of interest (JM-MA####.htm, where MA#### is the name of the .mol file created above). Edit the html title and header tags and add the filename in the Jmol load call using WordPad or Notepad, being sure the file is saved with the same format as before (i.e., do not use MS Word). Upload both the .htm and .mol file to the JMOL folder on the showme server ( using the WinSCP v3.82 program. Add the .htm file to the wiki page and be sure to test the molecule display.

File Downloads