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.
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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.
That’s a great task for analyzing protein structure! To show the interactions between chains B and E in PDB 1TUP, 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 1TUP, and hit the return key.
b) Click the menu ‘Analysis’.
c) Click ‘Defined Sets’ to open the list of predefined sets.
d) Click on ‘1TUP_B’ to select chain B.
e) Repeat step (c), then click on ‘1TUP_E’ to add chain E to the selection. Now, both chains B and E 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 ‘1TUP_B’ and the second set should be ‘1TUP_E’ (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=1TUP to open the structure.
b) Use the command select sets 1TUP_B,1TUP_E to select both chains B and E.
c) Use the command line graph interaction pairs | 1TUP_B 1TUP_E 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=1TUP&command=select+sets+1TUP_B,1TUP_E;+line+graph+interaction+pairs+|+1TUP_B+1TUP_E
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.
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 1TUP, and hit the return key.
b) Click the menu ‘Analysis’.
c) Click ‘Defined Sets’ to open the list of predefined sets.
d) Click on ‘1TUP_B’ to select chain B.
e) Repeat step (c), then click on ‘1TUP_E’ to add chain E to the selection. Now, both chains B and E 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 ‘1TUP_B’ and the second set should be ‘1TUP_E’ (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=1TUP to open the structure.
b) Use the command select sets 1TUP_B,1TUP_E to select both chains B and E.
c) Use the command line graph interaction pairs | 1TUP_B 1TUP_E 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=1TUP&command=select+sets+1TUP_B,1TUP_E;+line+graph+interaction+pairs+|+1TUP_B+1TUP_E
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.
In the URL method section, you will find “The full sharable URL”. If you copy that URL and paste it into a web browser, you will get your custom view:
