JmolPreparation

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 (http://showme.physics.drexel.edu/owens/JMOL) using the [|WinSCP v3.82] program. Add the **.htm** file to the wiki page and be sure to test the molecule display.


 * File Downloads**