I wanted to see the h bond interaction within a protein so I used swiss pdb viewer. Generally it gives only green dotted line as h bonds, but it also gave purple colored dotted line. Can anyone tell me what those purple lines indicate?
Sweta Kumari
Ma'am, you may use pymol, discovery studio visualizer or ligplot+ for analyzing the hydrogen bond. In discovery studio visualizer, there is option to save images in required resolution (2D and 3D). Same can be done using ray command in pymol.
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