Biochemistry Online: An Approach Based on Chemical Logic

Chime and Jmol Files

01/06/2009

The list below contains modeling tutorial files that are available from Biochemistry Online: An Approach Based on Chemical Logic. Some are links to outside files, but the majority have been created specifically for this course, mostly by students.   During the summer of 2006, I will converted most of the Chime files to Jmol format, which does not require the Chime plugin.  It can run on any browser that is Java enabled, on any computer, including Macs, Unix, and Linux systems.  The graphics are better as well.  The structural coordinates for the molecules below were downloaded directly from the Protein Data Bank without further refinements or energy minimizations.  In some, molecules not relevant to the displays (water, etc) have been deleted from the pdb files.  These files have been made over a five year period.  The earlier ones are less interactive and have contain less written information.  As most are from students, the very in the amount of supportive information provided.

Chime Instructions: If you are working at a PC in a public access area, you can use a internet browser plug-in (which is already installed in those areas) called Chime.   It will allow you to view and manipulate molecular models interactively on your computer.   You should be able to see and rotate your molecule by placing the mouse cursor in the black window and using the commands given below:

• Hold down the left mouse button and move the mouse around to rotate the molecule
• Hold down both the shift key and the left mouse button, then move the mouse up to zoom out or down to zoom  in
• Hold down both the control button and the right mouse button, then move the mouse to translate the molecule on the xy axes

In addition, you can change the rendering of the molecule by moving the mouse cursor within the area of the molecule. Click and hold the right mouse button, and a new menu will appear that will allow additional manipulation of the molecule. Experiment with these commands.

 Jmol Instructions: TBA

Jmol files below highlighted in

General Sites

• World Index of BioMolecular Visualization Resources
• Molecules in Motion

General Jmol Sites

• Molecules in Motion

• JMol

• Jmol web sites
• Jmol demos

• Awesome tutorial! 

• 2nd awesome tutorial on surfaces

• Jmol 11.4 script commands

• Online Molecule Museum
• Organic
• Another organic chem site
• 5/19/08    Jmol Organic mechanisms
• Jmol Documentation and Websites
• Jmol Documentation
• Updates to Jmol
• Popup window for testing Jmol commands
• 5/19/08:  Molecular Science Lab:  CHO, Lipid, Protein structures
• 5/19/08    MolViz
• 5/19/08    MolViz Top 5
• 5/19/08    Protopedia:  The collaborative, 3D encyclopedia of proteins and other molecules
• 5/19/08    Jmol tutorial templates
• 5/19/08    Jmol autoring template