Department of Natural Sciences The Hebrew University of Jerusalem The Open University of Israel Shoham - The Center for Technology in Distance Education home page Continuous Symmetry Measures

Jmol help

Jmol is an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. Jmol provides its own menu that enables users to toggle between different molecule display options. Right click the mouse to open the menu. Some of the menu options are listed below. For more information on Jmol, see http://jmol.sourceforge.net.

  1. Model - this option is active when the file contains more than one model. Use this option to toggle between models or display them all together.


  2. Select - use this option to select all atoms or a specific atom. Select an atom or atoms to change the color, to display labels, or to execute other options with respect to part of the molecule.


  3. Style - opens a sub-menu containing the following items:


    1. Scheme - several display formats are avaliable. Among them are:
      • Ball & Stick - sticks represent chemical bonds and balls represent atoms.
      • Wireframe - lines represent chemical bonds and vertices represent atoms.
      • Sticks - sticks represent chemical bonds and vertices represent atoms.
    2. Atoms - choose show hydrogens to show or hide hydrogen atoms. Click off to hide all atoms. Control the size of balls in all atoms, using the van der Waals 15%-100% option.
    3. Labels - select the appropriate option to display atom symbols and serial numbers.
    4. Bonds - choose on or off to show or hide chemical bonds. Select thickness of bonds from 0.10Å to 0.30Å.


  4. Color - this menu controls the color scheme of atoms, bonds and other items on the screen. The default color scheme is the CPK. This scheme was developed by Corey and Pauling and later enhanced by Koltun (hence the name CPK), and initially used to mark atoms in plastic models. Atom colors are specified on the Jmol website Help page: http://jmol.sourceforge.net/jscolors.


  5. Zoom - changes the molecule size on the Jmol screen. Size can also be changed using the mouse wheel.


  6. Spin - rotates molecule automatically around the Z-axis. Click On to start and Off to stop.


  7. Measurement - use this sub-menu to display bond lengths, bond angles and torsion angles. To display bond length, choose click for distance measurement. Then click on two atoms on the screen. Note that the chosen atoms are displayed on the status bar of the html page. The bond length will appear on the screen. Click on the same two atoms to delete the bond length. To display bond angle, choose click for angle measurement. Then click on three atoms on the screen. To display torsion angles, choose click for torsion (dihedral) measurement. Then click on four atoms on the screen. Choose delete measurements to remove all measurements from the screen.


  8. Show - use this sub-menu to save a file from the Jmol window. Choose file content to open a small window with the content of the file. Then copy and paste the text to a text editor (e.g., Notepad) and save it with the suffix pdb.





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