This is a short tutorial on how to use VMD to visualize molecules and perform some basic analysis. Before you start, make sure to have downloaded and installed VMD.
These steps will be on how to load molecules into VMD. We will use the example of 6vw1.
Download the protein structure of 6vw1 from the protein data bank.
Next we can launch VMD and load the molecule into the program. In
VMD Main, navigate to
File > New Molecule. Click
Browse, select the molecule (
6vw1.pdb) and click
The molecule should now be listed in
VMD Main as well as the visualization in the
Section to be moved
For VMD, there is no specific keyword to select glycans. A workaround is to use the keywords: “not protein and not water”. To recreate the basic VMD visualizations from the module of the open-state (6vyb) of SARS-CoV-2 Spike, use the following representations. (For the protein chains, use Glass3 for Material).
The end result should look like this: