10.4 2D Interaction Diagram
10.4 2D Interaction Diagram
For docking results (these should be optimised structures), there are multiple ways provided to visualise the interactions in a 2D-diagram for clarity. In this tutorial, we chose Discovery Studio Visualizer (an academic-free software) for this purpose,
1. Download
Register your academic email on the main website of Discovery Studio Visualizer for access
2. Main interface
3. Open your structures
To do this, you can simply drag your pdb files into the interface and it will work (In fact, any file in pdb format will work). In this case, we chose a roughly pre-processed 4uag pdb file (downloaded from Protein Data Bank, with hydrogen added, water removed).
4. Choose the “Show 2D diagram” function and it will open like following:
5. To optimise the positions of residue illustrators and molecular bonds/atoms:
Step1: click on the ball-shaped residue illustrator (it will change colour to yellow as below and this means it is ready to be edited)
Step2: “CTRL+Left-Click” (Mac should be “Command + Left-Click”) to select and drag it around (so that interaction lines won’t overlap that much as the original one).
Step 3: click on a single atom and it will show as a black hollow dot, meaning it is ready to be edited. Then, drag it around by applying the same technique in step 2.
6. Save the image
