Instructions for Viewing Molecules with Chime

Chemistry Department - CSB/SJU

Mouse Commands

When you click on any of the molecules listed below, a black window containing the molecule will appear in your browser.  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. 

More Sophisticated Ways to Change the Display

right click on the actual molecule, and a new selection of commands will pop up. You can then select an appropriate command with a click of the left mouse button. A check will apear by command indicating that you have selected it. The important options are shown below along with a brief comment in red about the use of some of them.

File

• Save Molecule As - it would seem like you could save a rendering of your molecule this way but it doesn't seem to work for me.

Edit

• Copy Chime Script - This might be useful if you went to someones else's Chime page (several are referenced below) and see something particularly interesting for which you would like to use the commands. You could then copy the Chime script and paste it into your page1.html document from the HTML editor of Front Page and see if it works for you. It's worth a try, but if you are trying to copy a bunch of Java code, I don't think it will work.

Rotation

Display - Can't do much more than what's available with buttons from the command window.

• Wire
• Stick
• Ball
• Space Fill
  • Van der Waals Radii
• Backbone
• Ribbon
• Strands
• Cartoon

Options

• Display Hydrogens - Very useful since X-Ray structures don't have hydrogens since they don't have enough electrons to diffract x-rays. However, by placing them in, H bonds make more sense since they will come from a H on a N or O, and not from an N or O to a N or O.
• Display Hydrogen Bonds
• Display Disulfide Bridges - Useful to see how many and where the disulfides are
• Dot Surface
  • Van der Waals
  • Conally Surface - This is the water-accessible surface of the molecule, as we encountered in Quanta/Charmm.
• Labels
• Sprout Hydrogens - same as display H's above, I think.
• Stereo Display - Believe it or not, you can see these images in 3D if you can cross you eyes. This command splits the image into two which if viewed with crossed eyes, or flayed eye, will result in the appearance of a 3D image.

Color -allows you to color code by something other than the originary red for O, blue for N, white for H, etc, CPK color system.

• Monochrome
• CPK
• Amino Acid
• Shapely
• Group
• Chain
• Temperature
• Structure

Select - This is the most imporant of all these commands because it allows you to select only certain parts of the display for showing. You will have to experiment on your own with this, but just looking at the commands allows you to see the possibilities. Notice that you can select all, invert a selection (i.e. show everything you didn't select), or hide a selection.

• Select All
• Mouse Click Action
• Highlight Selection - this must be clicked to see the results of your selection process
• Invert Selection
• Hide
  • Hide Selected
  • Hide Not Selected
• Change Color
  • (to a whole series of possilbe colors)
• Modify Selection Mode
  • Replace Selection
  • Add to Selection
  • Add common to Selection
  • Subtract from Selection
• Chain
  • A
  • B
• Residue
  • (alll the amino acids in a file are listed)
• Atom
  • (select different atoms - alpha C, H, O's etc)
• Hydrogen
• Nonhydrogen
• Hetero
  • Hetero
  • Solvent
  • Nonsolvent
  • Water
  • Ions - this should be great for displaying a bound ion
  • Ligand - this should be great for displaying a bound ligand
• Protein
  • Protein
  • Amino
  • Large
  • Medium
  • Small
  • Alpha Carbon
  • Backbone
  • Bonded
  • Buried
  • Helix
  • Sheet
  • Side Chain
  • Surface
  • Turn
  • Acidic - great to show areas of localized charge density
  • Acyclic
  • Aliphatic
  • Aromatic
  • Basic - great to show areas of localized charge density
  • Charged
  • Cyclic
  • Cystine (disulfide bond)
  • Hydrophobic - great to show areas of localized hydrophobicity
  • Neutral
  • Polar
• Nucleic Acid
  • Nucleic
  • DNA
  • Bacbone
  • AT
  • CG
  • Purine
  • Pyrimidine
• Display List
  • Create Molecular Surface - This takes a while to generate, and doesn't offer a significant advantage over van der Waals or Conolly surfaces.
  • Color
    • Electrostatic Potential - Should be great to show how differences between regions of net postive charge and regions of net negative charge give rise to a net electrostatic potential
    • Lipophilic Potential - Should be great to show how differences between regions of net high hydropathy and regions of net low hydropathy give rise to net hydrophobic moment
    • (various colors listed)

GREAT SITES USING CHIME

• World Index of BioMolecular Tutorials in Chime
• The Online Macromolecule Museum at Kenyon College
• WWU Virtual Molecular Model Kit - Teaching Organic Structures on the Web
• Molecular Models for Biochemistry
• 3D Structural Database of Pharmaceuticals
• A Chime tutorial on VSEPR theory
• IR Animations
• Infrared Spectroscopy and Modes of Vibrations
• Some organic reaction animations
• Molecules with Flavor
• Database of Small Biological Molecules