Laboratory 2 Visual molecular dynamics

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Structures that can be found on Protein DataBank. Most of the structures are obtained with Cryo-EM. An interesting part of the website is the “Learn” part. A lot of material is present. The .pdb file format is readable with a text editor, there are keyword for the amminoacids names. CRYST1 gives information about the unit cells of each atom. The first 3 numbers are related to the axys and the 3 90s are the angles. The CRYST1 keyword is found at the beginning of each line. The ATOM keyword you have several items of the line. Serial number, name, chainID and so on and so forth. The atom name tells what atom it is, and also the coordinates are stored. This information is stored into specific columns. If few characters are deleted, even if blank spaces, the file is corrupted. In the main representations, hydrogen atoms are not displayed, since they are not easily scattered in crystallography. Oxygen is in red, carbon is green. SWITCHING MODE The Mouse mode can be switched in order to move the molecule, scale it and so on. By default VMD uses a perspective representation, but it is worth to switch to an orthographic representation. GRAPHICS Representation could be changed. In some of them, isolated red dots can be seen, these are water molecules. The ribbon representation highlights the presence of strucutural motifs, such as alpha-helices or beta sheets. Coloring methods can also be explored. Secondary structures could be easily identified, for example. SECTION 1.3.3 – Different Selection Different atoms could be selected or different structures, using also Boolean operators. For example, I can also display sidechains a residues “sidechain and (residue 0 1 2 3 4 5) “. NOTE that you can store different representations and combine them together. We can combine for example…