iCn3D Fundamentals
Author: Alexa M. Salsbury, PhD
iCn3D Shortcuts and 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](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image002.png)
3. Orient yourself (see iCn3D Shortcuts for help)
![Screenshot from the iCn3D website, ITUP biomolecule with chain coloring](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image004.png)
4. Hover over structure with your mouse to view residues
![Screenshot from the iCn3D website, ITUP biomolecule, chain coloring](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image06.jpg)
5. Select > Select on 3D > Atom to see atomistic details
![Screenshot from the iCn3D website, Select > Select on 3D > Atom](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image008.png)
6. Hover over structure with your mouse to view atoms
![Screenshot from the iCn3D website, ITUP biomolecule, LEU289@N](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image010.png)
7. Change styling with Style > Sidechains > Lines
![Screenshot from the iCn3D website, ITUP biomolecule, Style > Proteins > Ribbon](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image012.png)
8. Explore different Style options and color the biomolecule to your liking (ex. Nucl. Bases > Stick)
![Screenshot from the iCn3D website, ITUP biomolecule, Style > Nucl. Bases > Stick](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image014.jpg)
9. Make specific selections with Analysis > Defined Sets
![Screenshot from the iCn3D website, ITUP biomolecule, Analysis > Defined Sets](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image016.png)
10. Select nucleotides and change color with Color > Rainbow
![Screenshot from the iCn3D website, ITUP biomolecule, Select sets > nucleotides](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image18.png)
11. Select residues by sequence with Analysis > Seq. & Annotations
![Screenshot from the iCn3D website, Analysis > Seq & Annotations](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image020.png)
12. Uncheck annotations and click Details
![Screenshot from the iCn3D website, Sequences and Annotations](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image022.png)
![Screenshot from the iCn3D website, Sequences and Annotations](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image024.png)
13. Highlight residues from the sequence to select
![Screenshot from the iCn3D website, Sequences and Annotations](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image026.png)
14. Clear selections and close or minimize Seq. & Annotations when not using
![Screenshot from the iCn3D website, Sequences and Annotations](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image028.png)
15. Explore ion interactions with Select > By Distance
![Screenshot from the iCn3D website, Select > By Distance](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image030.png)
16. Choose ions, set sphere radius to 5 Å, choose non-selected, and click on Display
![Screenshot from the iCn3D website, Select by distance](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image032.png)
17. Save the selection by Select > Save Selection and give name like resi_5a_zn
![Screenshot from the iCn3D website, Select > Save selection](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image034.png)
![Screenshot from the iCn3D website, Save the selected](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image036.png)
18. View your newly named selection resi_5a_zn and View > View Selection
![Screenshot from the iCn3D website, Select sets resi_5a_zn](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image038.png)
![Screenshot from the iCn3D website, View Selection](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image040.png)
19. Click on View Full Structure to see entire biomolecule again
![Screenshot from the iCn3D website, View Full Structure](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image042.png)
20. Change your background color with Style > Background > White
![Screenshot from the iCn3D website, Style > Background > White](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image044.png)
![Screenshot from the iCn3D website, ITUP biomolecule with a white background](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image046.png)
21. 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](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image048.png)
22. Save your rendering as an interactive link with File > Share Link and copy
![Screenshot from the iCn3D website, File > Share Link](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image050.jpg)
![Screenshot from the iCn3D website, Copy a Share Link URL](/ncbi/workshops/2022-10_3d-molecular-structures/images/fundamentals/image052.jpg)
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Last Reviewed: October 18, 2022