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Click to Identify Atom

Clicking on any atom should report the atom's identification into the slot at the top. This may not work consistently with SGI Chime 0.9e. This works only for spacefilled atoms or backbones (with sharp angles); it does not work for smoothed backbone traces or cartoons. [Close]

Cartoon (Initial View)

Each chain is assigned a different color. The CPK color scheme is applied to ligands. Only protein, DNA, and RNA chains are shown as cartoons. (Other chains are shown spacefilled, such as polysaccharides, unless ligands are turned off.) 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. [Close]

Backbone

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

Protein

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. [Close]

DNA/RNA

DNA and RNA are shown spacefilled with the following mnemonic color scheme:

Brown (Backbone) Bases: Green Carmine Azure Tweety bird pUrple

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Secondary Structure

Protein, DNA, and RNA are shown as cartoons colored as follows:

Helix Strand/Sheet Turn Other; DNA, RNA

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

Termini

Protein, DNA, and RNA are 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. [Close]

Ligands

In this display, "Ligands" are defined as everything other than protein, DNA, RNA, or water. Ligands are shown spacefilled with the CPK (Corey Pauling Kultin) color scheme adapted from pre-computer physical models. The main elements are:

Carbon Hydrogen Oxygen Nitrogen Phosphorus Sulfur Iron

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Water

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. [Close]

Spin, Zoom

Spin can be turned on and off with the Chime Menu (click on the "MDL" at the lower right to get the menu; SGI: right click). 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). [Close]