Structures
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Manipulate a structure with Cn3D - Part 2

  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 using the Show/Hide menu and the annotation options. Add labels. Remove the B chain from view.

Analysis/Comments back to top

It takes a bit of practice to become familiar with the variety of viewing options provided by Cn3D. Often it is valuable to focus on a specific part of the molecule. Labeling amino acids can provide orientation and identification. These and other options can help produce a picture of the structure that can be used for teaching or publication.

Flow Chart back to top

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

Step By Step Guide back to top

Cn3D

  • From the Show/Hide menu, choose 'Pick Structures'. In the resulting dialog box, click on the B chain domains to deselect them (remove the blue highlighting), then click on 'done'.
  • Select (double-click to highlight in yellow) the amino acids you wish to annotate. Then use the 'annotation' option in the Style menu to open the annotation dialog box. Click on 'add new' then name the new annotation. Use the 'edit style' link, then choose the label tab to locate the options for applying a label to the amino acids. Selecting to label every "1" amino acid will label all of them. Labeling every "2" amino acids will label every second (every other) amino acid.

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Return to Exercises List		 Revised 08/08/2007