vizomics.org developed an "AI Tutor for iCn3D" tool to use AI as a tutor to shows step-by-step instructions about how to build a custom 3D view in iCn3D with five methods: Interactive, Sharable URL, Jupyter Notebook, Node.js script, and Python script. This tool was added as a link in the Help menu of iCn3D.

For example, if you click "AI Tutor for iCn3D" and ask "show interactions between chains A and B in PDB 1KQ2", you will get the following answer from the AI:

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That's a great task for analyzing protein structure! To show the interactions between chains A and B in PDB 1KQ2, you will open the structure, select the two chains, and then use the 'Analysis > Interactions' menu. Here are the two typical methods:

1. Interactive Method

This method involves navigating the iCn3D menus in your browser to select the chains and view the interactions.

a) Open iCn3D at https://www.ncbi.nlm.nih.gov/Structure/icn3d, input the PDB ID 1KQ2, and hit the return key.

b) Click the menu 'Analysis'.

c) Click 'Defined Sets' to open the list of predefined sets.

d) Click on '1KQ2_A' to select chain A.

e) Repeat step (c), then click on '1KQ2_B' to add chain B to the selection. Now, both chains A and B are selected.

f) Click the menu 'Analysis' again.

g) Click 'Interactions'.

h) In the "Interaction Pairs" section of the popup window, the first set should be '1KQ2_A' and the second set should be '1KQ2_B' (or vice versa).

i) Click the "2D Interaction Network" button to display a new window showing the network of interactions (such as hydrogen bonds, salt bridges, van der Waals) between the two chains, while the 3D viewer will also highlight these interactions.

2. URL Method

This method creates a single URL that automatically loads the structure and executes the commands to select the chains and show their interactions. The required commands are:

a) Use the URL parameter ?mmdbafid=1KQ2 to open the structure.

b) Use the command select sets 1KQ2_A,1KQ2_B to select both chains A and B.

c) Use the command line graph interaction pairs | 1KQ2_A 1KQ2_B to display the interactions between the two chains in a 2D network and show them in 3D.

The full URL is: https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbafid=1KQ2&command=select+sets+1KQ2_A,1KQ2_B;+line+graph+interaction+pairs+|+1KQ2_A+1KQ2_B

Other Methods

You can also achieve the same result using the following methods:

Jupyter Notebook: Install icn3dpy and use the same URL parameters/commands.

Node.js script: Install the icn3d package and run a script like general_id_cmd.js with the commands.

Python script: Use a tool like selenium to drive the web page with the generated URL.

You can find more tutorials, including Virtual Reality (VR) and Augmented Reality (AR) usage, at https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#videos.