Mod:Hunt Research Group/jmol visualisation

how to add jmol structures

first make a coordinate file

this can be a .xyz coordinate file or a .mol file saved using gaussview

using gaussview

open your molecule in gaussview

choose save

in the options choose save as a mol file

here is what gaussview saved for my file

Title Card Required

Created by GaussView 4.1.2
  4  3  0  0  0  0  0  0  0  0  0    0
    0.0000    0.0000    0.0000 B   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.1945    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0345   -0.5973    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0345   -0.5973    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0

making an xyz file

this has 3 sections

1. first line: number of atoms in the molecule
2. second line: comments or title
3. following lines: atomic symbol followed by xyz coordiantes

4
BH3 molecule
 B    0.00000000    0.00000000    0.00000000
 H    0.00000000    1.19452732    0.00000000
 H    1.03449101   -0.59726366    0.00000000
 H   -1.03449101   -0.59726366    0.00000000

how to make the jmol window and button

load your molecule to the wiki, eg choose "upload file" from the menu to the left and follow the instructions

add the following script to your wiki replacing molecule_1.mol with your file name (molecule.mol or molecule.xyz), and changing the text

<jmol>
<jmolAppletButton>
<uploadedFileContents>molecule_1.mol</uploadedFileContents>
<text>Molecule 1</text>
</jmolAppletButton>
</jmol>