Flowchart for Visualizing Protein Crystal Structure using Cn3D

Enter Entrez Protein: (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein)

In the “Search window” copy and paste or type the following: per2 NP_073728.

Select the “Conserved Domains” link in the right column of the retrieved file.

Select the “PAS” hyperlink (red box).

Select “View 3D Structure” and choose Cn3D from the pull down menu.

The program Cn3D will show you two windows. One showing the 3D structure of two aligned proteins and another just below it that show the amino acid sequences of several proteins: 3PYP, 1DRM A are the ones in the 3D viewer.

Click and hold over protein structures to move and rotate the digital models.

To view one at a time select “Show/Hide” then “Pick Structures” and highlight one of the proteins.

Select “Style” then “Rendering Shortcuts” and then any of the options to change modeling styles.

In the “Sequence Viewer” window showing amino acid alignments, highlight some of the amino acids in colored, capital text from either 3PYP or 1DRM A. The corresponding amino acids in the 3D model will turn yellow. This will aid in determining structural homology.