VMD is a molecular modeling and visualization software, mainly used to analyze experimental data from molecular dynamics simulations. It also includes modules for processing length and mention related data, visualizing and analyzing trajectories, adding arbitrary graphics, and exporting to formats that other software can utilize such as POV-Ray, PRMan, VRML, etc. The user can run Tcl and Python scripts for batch operations and can interact with other programs via Tcl/Tk.
First, load the pdb protein molecule file through the File menu
In the main VMD window, select "Graphics>>Representations..." menu option to open the Graphics Representation window. In the Draw style, set the Coloring Method to Secondary Structure and the Drawing Method to NewCartoon to get the cartoon display mode protein.
The window also has a text input area for Selected Atoms, where you can enter specific words to select only a certain part of the molecule to be displayed. For example, delete the original word all, type helix, and click the Apply button in the lower right corner (or press Enter). the OpenGL display window will only show the helix part.
If you don't know what words to enter at first, you can also select the Selections option in the window, there is a Singlewords list below, double-click one of the options to enter, and then click Apply.
In addition, some simple Boolean operators can be entered to define the displayed area. For example, if you need to observe parts other than the helix and beta-fold, just type: not helix and not betasheet in the Selected Atoms input field and press Enter.
Further, we can also display only one or a few amino acids from the protein. In the Selections option, choose resname for Keyword and LYS for Value (again, double-click to enter into the Selected Atoms input field). Then only lysine can be displayed in the OpenGL display window (the drawing style below is CPK and the coloring method is Name).
If you enter water in the Selected Atoms input field, you can display the 58 water molecules around the protein (actually the hydrogen atoms are not shown).
If you enter water and within 3 of protein, you can also display all water molecules that are within 3 Å of the protein, which is also very convenient to operate.
Finally, try entering the following phrase in the Selected Atoms input field and press Enter to see what results you get.