Updated July 14, 2022.
Proteins. These proteins are quite interesting and getting to know them through VMD allows you to start to understand how they function.
- Using one of the proteins (1fo4, 2pah and 1phz together, see this link) make a working PDB/PSF pair which separates each type of molecule (protein, water+ions, ligand, if any), or simply the protein (including any chains) into it's own segment(s). Make sure that the protein and other molecules are not modified (no patching). You could also find another protein. Guidelines for this: less than 10,000 atoms, regular residues, and only water, sodium, iron, magnesium or some other metal. This should be a SINGLE PDB and a SINGLE PSF, with the separate chain information within the file(s). (15 Points)
- Create a visual representation of the protein system which makes the protein a surface of some neutral color, and makes the other species appropriate models (CPK or VDW). Color the surface of the protein such that it is a different color when a water molecule is within 5 angstroms of the surface, and another color when an ion is within 5 angstroms. (5 Points)