AI Tutor for iCn3D
This AI tutor for iCn3D works as a tutor to show step-by-step instructions about how to build a custom view with five methods: Interactive, Sharable URL, Jupyter Notebook, Node.js script, and Python script.
Launch AI Tutor, or scan 
to launch.
Once the page with the title “AI Tutor for iCn3D” appears, you can ask any questions about 3D biomolecular visualization in any language. One example question is “show interactions between chains B and E in PDB 1TUP”. The AI Tutor will provide the following answer.
You want to display the 2D interaction network between chains B and E of PDB structure 1TUP.
—
Interactive method
1. Open iCn3D at https://www.ncbi.nlm.nih.gov/Structure/icn3d/ and enter the PDB ID 1TUP, then press Return.
2. Click Analysis > Defined Sets — a popup appears listing predefined sets. Click 1TUP_B to select chain B.
3. Click Analysis > Defined Sets again and click 1TUP_E to select chain E (this adds it to the current selection).
4. Click Analysis > Interactions — in the popup, set the first set to 1TUP_B and the second set to 1TUP_E, then click 2D Interaction Network to display the interactions between the two chains in a separate window.
—
URL method
1. Use ?mmdbafid=1TUP to open the structure.
2. Use the command line graph interaction pairs | 1TUP_B 1TUP_E to show interactions between chains B and E.
Full URL:
https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbafid=1TUP&command=line+graph+interaction+pairs+|+1TUP_B+1TUP_E
—
Other ways to do this
– Jupyter Notebook (icn3dpy): https://pypi.org/project/icn3dpy/
– Node.js script (icn3d + general_id_cmd.js): https://github.com/ncbi/icn3d/tree/master/icn3dnode
– Python script (selenium + batch_export_ss.py): https://github.com/ncbi/icn3d/tree/master/icn3dpython
—
For video tutorials, see https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#videos
—
Interactive method
1. Open iCn3D at https://www.ncbi.nlm.nih.gov/Structure/icn3d/ and enter the PDB ID 1TUP, then press Return.
2. Click Analysis > Defined Sets — a popup appears listing predefined sets. Click 1TUP_B to select chain B.
3. Click Analysis > Defined Sets again and click 1TUP_E to select chain E (this adds it to the current selection).
4. Click Analysis > Interactions — in the popup, set the first set to 1TUP_B and the second set to 1TUP_E, then click 2D Interaction Network to display the interactions between the two chains in a separate window.
—
URL method
1. Use ?mmdbafid=1TUP to open the structure.
2. Use the command line graph interaction pairs | 1TUP_B 1TUP_E to show interactions between chains B and E.
Full URL:
https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbafid=1TUP&command=line+graph+interaction+pairs+|+1TUP_B+1TUP_E
—
Other ways to do this
– Jupyter Notebook (icn3dpy): https://pypi.org/project/icn3dpy/
– Node.js script (icn3d + general_id_cmd.js): https://github.com/ncbi/icn3d/tree/master/icn3dnode
– Python script (selenium + batch_export_ss.py): https://github.com/ncbi/icn3d/tree/master/icn3dpython
—
For video tutorials, see https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#videos
In the URL method section, you will get the following custom view if you click the “Full URL”:
