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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


3. Orient yourself (see iCn3D Shortcuts for help)
Screenshot from the iCn3D website, ITUP biomolecule with chain coloring


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. Change styling with Style > Sidechains > Lines
Screenshot from the iCn3D website, ITUP biomolecule, Style > Proteins > Ribbon


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

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


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


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


12. Uncheck annotations and click Details
Screenshot from the iCn3D website, Sequences and Annotations


Screenshot from the iCn3D website, Sequences and Annotations

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


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


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


16. Choose ions, set sphere radius to 5 Å, choose non-selected, and click on Display
Screenshot from the iCn3D website, Select by distance


17. 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

18. View your newly named selection resi_5a_zn and View > View Selection
Screenshot from the iCn3D website, Select sets resi_5a_zn


Screenshot from the iCn3D website, View Selection

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


20. 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

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


22. 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

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Last Reviewed: October 18, 2022