iCn3D Skill: Alternative Rendering and Saving Files
- Page ID
- 114612
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- PDB ID: 1xww
- Protein: Low molecular weight protein tyrosine phosphatase
- Activity: hydrolyzes Tyr-OPO32- phosphoester bond
- Description: single chain, bound SO42- (competitive inhibitor), bound glycerol (nonspecific stabilizer)
Alternative Rendering
Load Structure and Mouse/Trackpad Controls
- Open iCn3D - https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html
- For a simple menu, use the dropdown: File > Customize Menus > Simple Menus.
- In the Please input MMDB or PDB, enter 1xww. Press enter or click load biological unit.
- Default render is ribbon (cartoon) with black background and small molecules shown as sticks. Hover over objects with the mouse to reveal their identity.
- From the top menu bar, choose Style, Protein, then try some of the available choices:
- For your favorite protein styles, select Color by left-clicking on the top menu, then pick available choices. Try:
- Secondary, Sheets in Yellow
- Charge
- Hydrophobicity
- Under Style, choose Protein → Ribbon. Under Color, choose Secondary, Sheets in Yellow before the next step.
- To view sidechains, Style, Side Chains, Stick (they will remain the same color as secondary structure for now)
- Color for SO42- and bound glycerol will default to CPK coloring (key below)
- Convert back to cartoon (Style, Side Chains, Hide)
Saving Files
- Style, Background, Transparent
- Saving Files: There are several ways to save your work. The first option below saves a PNG image, the second creates a share link
- File, Save Files, iCn3D PNG image, original size; Give it a name. Can be reloaded in iCn3D with File, Load, iCn3D PNG IMAGE
- File, Share Link, Save Lifelong Short URL. Copy and paste this link to share your work.
Pre-Rendered Model Link
To check your work (or if you got stuck during any of the steps above) catch up using this link: https://structure.ncbi.nlm.nih.gov/icn3d/share.html?CgfEnF27TN7aYQpr6
