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
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3. Orient yourself (see iCn3D Shortcuts for help)
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4. Hover over structure with your mouse to view residues
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5. Select > Select on 3D > Atom to see atomistic details
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6. Hover over structure with your mouse to view atoms
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7. Change styling with Style > Sidechains > Lines
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8. Explore different Style options and color the biomolecule to your liking (ex. Nucl. Bases > Stick)
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9. Make specific selections with Analysis > Defined Sets
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10. Select nucleotides and change color with Color > Rainbow
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11. Select residues by sequence with Analysis > Seq. & Annotations
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12. Uncheck annotations and click Details
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13. Highlight residues from the sequence to select
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14. Clear selections and close or minimize Seq. & Annotations when not using
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15. Explore ion interactions with Select > By Distance
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16. Choose ions, set sphere radius to 5 Å, choose non-selected, and click on Display
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17. Save the selection by Select > Save Selection and give name like resi_5a_zn
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18. View your newly named selection resi_5a_zn and View > View Selection
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19. Click on View Full Structure to see entire biomolecule again
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20. Change your background color with Style > Background > White
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21. Save your rendering as a PNG with File > Save Files > iCn3D PNG image
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22. Save your rendering as an interactive link with File > Share Link and copy
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Last Reviewed: October 18, 2022