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, or 3aic) make a working PDB/PSF pair which separates
each type of molecule (protein, water+ions, ligand, if any)the protein (including any chains) into it's own segment(s). Make sure that the protein and other molecules are not modified (no patching). (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)