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Star Republic: Guide for Biologists

Visulization of 3D structures on Mac

Although there are several Windows programs for visualizing 3D structures, few work well on Mac. Cn3D is one of the few that work well on both Mac and PC. Cn3D is developed by NCBI structure group for macromolecule structures in the NCBI's MMDB database. MMDB database contains data from the more familiar Protein Data Bank. The following instructions assume that users are using Mac OSX and Internet Explorer.

1. Go to NCBI Structure web site http://www.ncbi.nlm.nih.gov/Structure.

2. Search for structures. Change the database to Structure, type a protein name (e.g., p53) in the search field, and click on Go.

3. A list of the crystal structure data will be returned. Chose one structure and click on the link to individual structure.

4. A summary of the protein structure will be presented. If you already installed Cn3D for view 3D structure, click on the View 3D Structure button, your browser will call on Cn3D to display the structure.

5. If you have not installed Cn3D, click on the Get Cn3D 4.0 link. And download Cn3D for Macintosh.

6. You don't need to download Apple's OpenGL extension libraries, download only Cn3D-4.0.0.sit (or the most recent version).

7. After the completion of the downloading, Mac will automatically unstuff the sit file to a fold named Cn3D-4.0.0 Folder. Move this fold inside your Applications fold on your hard disk.

8. Within the Cn3D-4.0.0 Folder, you should see an application Cn3D. Testing it by double click on the Cn3D icon. The program will run stand-only. If you have already downloaded a MMDB structure file, use the Open function of Cn3D program to view the structure.

9. Going back to the Structure summary page at step 4. Click on View 3D Structure. The MMDB structure data will be downloaded to your computer. Your browser may ask you to pick an application. Set the application to Cn3D you just installed in your applications/Cn3D-4.0.0 folder.

10. Check your download manager for data your have downloaded. To view the same structure, you may not need to download the data each time. You may start Cn3D, and open the downloaded structure data file.