Structures
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Manipulate a structure with Cn3D

  Sample User Question
Analysis/Comments
Flow Chart
Step By Step Guide 		 

Sample User Question back to top

Manipulate the molecular structure of HIV-1 reverse transcriptase. Zoom in and out. Turn the structure around. View different rendering styles. Color the amino acids by hydrophobicity. Highlight neighboring amino acids and then locate them in the sequence window. Are they adjacent in the sequence?

Analysis/Comments back to top

It takes a bit of practice to become familiar with the variety of viewing options provided by Cn3D. Some combinations of rendering styles and coloration will be more useful than others, depending on the needs of the researcher. Also note the keyboard shortcuts available for zooming and moving the structure.

Flow Chart back to top

  1. Cn3D Molecular Structure Viewer - This program provides both menu options and keyboard shortcuts to manipulate 3-D structures.

Step By Step Guide back to top

Cn3D

  • First use the zoom in and zoom out menu options. Then use the keyboard shortcuts: "x" and "z".
  • Use the mouse and keyboard to move the structure across the viewing window. Hold down the shift key and drag the mouse.
  • Use the style menu to change the rendering styles and color options.
  • Double click on amino acids that are close together in the structure but not connected in the chain. They should turn yellow. Then look down at sequence window to find the yellow-highlighted amino acids. How far apart are they in the sequence?

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