Instructions for Obtaining and using CHIME 2

Obtaining Chime 2
Site: http://www.mdli.com/support/chime/chimefree.htm

Site: http://www.mdli.com/support/chime/mitch.htm
(or http://www.mdli.com/support/chime/chimefree.htm then "tutorials")
Mouse Control Summary
Summarizes rotate, translate, and zoom mouse functions

Option 2:

Site: http://www.umass.edu/microbio/chime/index.html then "Chime: How to Use It"
Mouse Control Summary
Summarizes rotate, translate, and zoom mouse functions.

There is no tutorial on the "menu" functions obtained with the right mouse button (Windows) or by clicking on the MDL symbol. The Menu and the submenus are as follows. The ones that are colored are particularly useful in the initial exercises with small molecules and they are briefly described below.

Menu

• File
  • Save Molecule As
• Edit
  • Copy
  • Copy Chime Script
  • Paste
  • Clear
  • Transfer to ISIS/Draw
  • Transfer to Sculpt
• 2D Rendering
• Animation
• Rotation
• Display
  • Wireframe
  • Sticks
  • Ball & Sticks
  • Spacefill
    • Van der Waals Radii
• Options
  • Display Hydrogens
  • Display Heteroatom Groups
  • Display Hydrogen Bonds
  • Display Disulfide Bridges
  • Display Wireframe Double Bonds
  • Dot Surface
  • Slab Mode
  • Specular
  • Shadows
  • Labels
  • Sprout Hydrogens
  • Stereo Display
• Color
  • Monochrome
  • CPK
  • Amino Acid
  • Shapely
  • Group
  • Chain
  • Temperature
  • Structure
  • User
  • Force Palette
• Sculpt Mode
• Select
  • Select All
  • Mouse Click Action
    • None
    • Identify
    • Distance
    • Angle
    • Torsion
    • Toggle Distance Monitor
    • Toggle Atom Label
    • Pick Center of Rotation
    • Toggle Atom's Selected State
    • Toggle Residue's Selected State
    • Toggle Chain's Selected State
  • Highlight Selection
  • Invert Selection
  • Hide
  • Change Color To
  • Modify Selection Mode
  • Model
  • Chain
  • Residue
  • Atom
  • Hydrogen
  • Nonhydrogen
  • Hetero
  • Protein
  • Nucleic
  • Display List
• Mouse
  • Open Mouse Control Help Page
• About

File/Save Molecule As
This function allows the image being viewed to be saved on your computer. and thus to be used later without being connected to the Internet. Be sure to note the directory and file name you assign so you can find the file again.

2D Rendering
This changes the display to a two dimensional version of the current view of the molecule. It is a good way to see the atom labels, but no manipulation of the image can be done. You get back to the three dimensional version by calling up the menu and selecting "3D Rendering".

Rotation
This turns on the continuous turning of the molecule about a vertical axis. The rotation continues until you select it again from the menu. Other commands can be used while the molecule is rotating.

Display This controls the way the 3 dimensional molecule is displayed and is quite useful.

Wireframe This is just a line drawing version, with atoms indicated as the points the lines meet.
Sticks Sticks are like wireframe, but thicker.
Ball & Sticks This is a particularly good way to view molecules. The atoms are now represented by colored balls, and the bonds are still lines between them.
Spacefill / Van der Waals Radii This mode represents the atoms "full size" which better represents the correct size of the atoms, but now there are no bonds visible because the atoms touch.

Options Some of these are self-explanatory and others are more specifically for biological macromolecules.

Specular and/or Shadow are ways of modifying the apparent lighting of the model. "Specular" puts highlights on the surface and "Shadow" adds shadows. These features add to the computation time required in displaying and rotating a molecule.
Labels turn on atom labels for atoms other than C and H. There are other ways to see the same information.
Display Hydrogens turns on or off the hydrogen atoms. For some structures there are so many H atoms that they obscure other atoms.
Slab mode is a way to cut through a molecule and only show the part of the molecule that is behind a "slab" parallel to the screen. Its use is demonstrated at http://www.umass.edu/microbio/chime/chimehow/chowslab.htm

Color This permits different color and coloring scheme choices.

CPK colors are a specific, standard code of colors that indicate the element. Monochrome selects white that sometimes makes the molecule clearer against a dark background. Other single colors can be chosen with Select/Change color to Select this is a large menu used to create complex displays by choosing different atoms for display and coloring in different ways. Many of the options are specific to biological macromolecules. Mouse click action This menu controls the way left clicking the mouse is used. Default is just to show the label of the atom at the bottom of the screen. Other choices allow measurement of distances and angles. Mouse/Open Mouse Control Help Page This shows the basic rotate/translate/zoom functions of the mouse. About This shows the version of Chime you are using, and some links to the makers of Chime.

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