Clicking on any atom should report the atom's identification into the slot at the top. This works only for spacefilled atoms or backbones (with sharp angles); it does not work for smoothed backbone traces or cartoons.

Each chain is assigned a different color. Upon clicking the botton the ligands are remove, but can be added with the "ligands on" button. Only protein is shown as cartoon. (Other chains are shown spacefilled, such as ligands) Alpha helices are shown as helical ribbons; beta strands have an arrowhead at the C terminus. "Flapping in the wind" during rotation is a rendering artifact, but serves to remind us that macromolecules are not static: they vibrate with thermal motion.

Wireframe

The wireframe view is the most basic possible, Chime performs no analysis of the protein.  Only the positions of the atoms and the bonds are show, making it kind of a useless view in terms of protein analysis. The backbone cannot be visually determined in larger proteins, such as hemoglobin or myoglobin.  The wireframe view first appears in "chain" distinct coloration, showing each chain of the molecule as a different color, but can be changed in the molecule menu.

Mixed

The mixed view is helpful in visualizing both the backbone as well as the sidechains.  This type of view is not often found in chime tutorials, but I find it to be particularly useful, and one of my favorites.

Straight sticks connect protein alpha carbon or polynucleotide phosphorus atoms. Color scheme is the same as for Cartoon.

Protein is shown spacefilled with the following color scheme:

Backbone Sidechains: Hydrophobic Polar Acidic Basic

Rationale: This color scheme derives from the CPK color scheme as follows. Hydrophobic = carbon; Acidic = oxygen; Basic = nitrogen. Polar but uncharged is shown as a mixture of oxygen (red) and nitrogen (blue), namely magenta. Backbone is polar but less likely (dark magenta) than sidechains to hydrogen bond to nonbackbone moieties since most backbone hydrogen bonding occurs within the backbone.

This view displays only the backbone of the protein in a simple white color.   It allows a nondistracting view of the associated ligands. 

Protein is shown as cartoon colored as follows:

Helix Strand/Sheet Turn Other; DNA, RNA

Often this color scheme is best viewed on a black background ("Background Off").

Protein is shown as backbones colored in a spectral rainbow sequence as follows:

Amino/5' ------------------ Carboxy/3'

Mnemonic: Blue = Cold = Old = Nitrogen/5' = Left = 1st synthesized. Red = Hot = New = Oxy/3'OH = Last to be synthesized. Colors are assigned globally by residue number so that only the longest chain has red and blue ends. Shorter chains usually have a blue end but the colors may not progress all the way to red.

In this display, "Ligands" are defined as everything other than protein, or water.  In the case of the hemoglobin quatramer, the ligands are four heme groups (shown below) and two Phosphorus.  Ligands are shown spacefilled with the CPK (Corey Pauling Kultin) color scheme adapted from pre-computer physical models. The main elements are:

  Here is the complete CPK color scheme used by Chime (and RasMol).

Water is shown spacefilled in CPK colors. In PDB files determined by crystal X-ray diffraction, hydrogens are missing unless they have been inserted in theoretical positions. Most water molecules present in protein crystals are mobile, and hence not resolved. Only the few tightly bound water molecules are resolved and hence shown in this display.  Since the position of the water molecules are not important in viewing the overlap of two proteins, they have been rendered unviewable.

Spin can be turned on and off with the Chime Menu, or the bottons on the side.  The Spin On/Off buttons on the display will work only with Chime version 2 (not available for Windows 3.1 or SGI).

Zoom can be controlled by dragging the mouse while holding down the Shift key. The Zoom On/Off buttons on the display increase or decrease the image size by 10% respectively per click. These buttons will work only with Chime version 2 (not available for Windows 3.1 or SGI). 

H bonds in red

This view displays all of the H bonds in red.  It is useful in the analysis  2^o structure stabilization.

Rotate to Center

This animation rotates the molecule 90 degrees along the X axis allowing to see down the middle of quatramers.  It then rotates the molecule 360 degrees along the Z axis, and then returns the molecule back to its original state. Very cool!

Fly Through

This animation rotates, then "flies" you through the center of deoxygenated hemoglobin, then back to your original view.  You can change the display type of the protein by selecting one of the view buttons above. The animation ends zoom =100.  Sit back and enjoy the ride. Even more cool than rotate to center.

Designed and written by Marc Roe & James Wollack '04

adapted from Eric Martz