Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

iCn3D Fundamentals

The objective of this exercise is to get familiar with NCBI's iCn3D. We will go over how to navigate, style, color, select, save, and share in iCn3D. The embedded links labled "follow" are designed to help participants in the live session follow the instructor's directions. If you fall behind or want to view an instructor created rendering, click these "follow" links. 

iCn3D Help Docs

 

1. Go to iCn3D: Web-based 3D Structure Viewer


2. Type "1TUP" and Click on Load Biological Unit
Screenshot from the iCn3D website, Load File 1TUP


3. Orient yourself (see iCn3D Shortcuts and Help Docs)

4. Hover over structure with your mouse to view residues
Screenshot from the iCn3D website, ITUP biomolecule, chain coloring

5. Select > Select on 3D > Atom to see atomistic details
 Screenshot from the iCn3D website, Select > Select  on 3D > Atom


6. Hover over structure with your mouse to view atoms
Screenshot from the iCn3D website, ITUP biomolecule, LEU289@N


7. Explore different Style options and color the biomolecule to your liking (ex. Nucl. Bases > Stick, Side Chains > Stick)
Screenshot from the iCn3D website, ITUP biomolecule, Style > Nucl. Bases > Stick

Follow


8. Make specific selections with Analysis > Defined Sets
Screenshot from the iCn3D website, ITUP biomolecule, Analysis > Defined Sets


9. Select nucleotides and change color with Color > Rainbow
Screenshot from the iCn3D website, ITUP biomolecule, Select sets > nucleotides


10. Select residues by sequence with Analysis > Seq. & Annotations
Screenshot from the iCn3D website, Analysis > Seq & Annotations


11. For a simplified view, uncheck annotations and click Details
Screenshot from the iCn3D website, Sequences and Annotations


Screenshot from the iCn3D website, Sequences and Annotations


12. Highlight residues from the sequence to select
Screenshot from the iCn3D website, Sequences and Annotations


13. Clear selections and close or minimize Seq. & Annotations when not using
Screenshot from the iCn3D website, Sequences and Annotations


14. Explore ion interactions with Select > By Distance
Screenshot from the iCn3D website, Select > By Distance


15. Choose ions, set sphere radius to 5 Å, choose 1TUP, and click on Display
Screenshot from the iCn3D website, Select by distance


16. Save the selection by Select > Save Selection and give name like resi_5a_zn
Screenshot from the iCn3D website, Select > Save selection


Screenshot from the iCn3D website, Save the selected

17. View your newly named selection resi_5a_zn and View > View Selection and render
 to your liking (ex. Style > Side Chains > Stick)

Screenshot from the iCn3D website, Select sets resi_5a_zn


Screenshot from the iCn3D website, View Selection

18. Click on View Full Structure to see entire biomolecule again
Screenshot from the iCn3D website, View Full Structure

Follow

19. Before saving, change your background color with Style > Background > White
Screenshot from the iCn3D website, Style > Background > White


Screenshot from the iCn3D website, ITUP biomolecule with a white background


20. Save your rendering as a PNG with File > Save Files > iCn3D PNG image
Screenshot from the iCn3D website,  Save File > iCn3D PNG Image > Original Size


21. Save your rendering as an interactive link with File > Share Link and copy
Screenshot from the iCn3D website, File > Share Link

Screenshot from the iCn3D website, Copy a Share Link URL


Page 1 of 1

Last Reviewed: April 14, 2023