CHM 579 Assignment #1

Molecular Graphics

Due on Monday, Jan 27 2020 at 3:29 PM

The objective of this assignment is three-fold: first, to become familiar with protein structures and the Protein Data Bank, second, to try some of the programs used to display protein structures, and third to learn how these programs can be used for research and understanding.

The Protein Data Bank

The Protein Data Bank, or PDB, is the best place to obtain 3-Dimensional structures of proteins, nucleic acids, peptides and other macromolecules. From their site, you can locate proteins by keyword searching or by entering the accession number for the structure file, like 1mba. Most of the structures in the PDB were determined by X-ray crystallography or NMR spectroscopy with a growing trend of using Cryo-EM. Details on the molecules in the structure file, how the structures were determined, pertinent research articles, etc. can be found on the web site but also in the pdb file itself.

PDB files are just formatted text files, so you can open them in a text editor or even Word and read them. There is a wealth of information there! The molecular viewing programs use the ATOM records in the file, which contain residue name, residue number, atom name and atom number - all of which are important when selecting molecules or parts of them to visualize. Often, the structure files include other molecules besides the protein, such as water molecules, nucleic acid and bound ligands.

Molecular Graphics Programs

There are quite a few programs used to view molecules.. Each has its advantages and disadvantages. We provide links to the programs discussed in the lectures (and their manuals/documentation) on the Programs Page.

  1. PyMol

    PyMol is a relatively new and very promising molecule viewing program developed by Schodinger . It is available for all Unix/Linux platforms, Windows and Mac OSX. It uses a combination of menus, a powerful selection sidebar, ( to demonstrated in the lab), and a rich command line interface. It has a logging feature to remember commands as they are executed, allows for scripting and has a nice movie feature. We have created a PyMol tutorial for you to get started with the program. There is also a tutorial on the PyMol website. Also check out the PyMol Wiki for more help and tips.
  2. Visual Molecular Dynamics (VMD)

    VMD is new and very promising molecule viewing program developed at University of Illinois at Urbana-Champaign. It is available for all Unix/Linux platforms, Windows and Mac OSX. It uses a combination of three windows: a terminal window, a viewing window and a main window. The terminal window is useful in that error messages and command output. The view window is where your molecules will appear, and the main window is where most of the controls for VMD are found. We have created a VMD tutorial for you to get started with VMD. We strongly encourage you to go through the VMD tutorial also which can be found on the VMD website, if you need more information to create this assignment. VMD is a very important tool which would be helpful for further assignments as well.
  3. MINT(optional)

    MINT is Virtual Reality(VR) visualization program that is currently under heavy development by ChopraLab. It uses cutting edge technology, such as the HTC Vive, to show 3D features of biologic molecules in novel ways. Instead of looking at a 2D image of 3D object, users are able to experience the true 3D nature of the protein in an immersive VR environment and manipulate the chemical environment around them using tools that were impossible just a few years ago.

There are a number of different molecular graphics programs out there (rasmol, molmol, swissPDBviewer, Chimera, to name a few) but we feel that Pymol and VMD together offer the best features for this course. You are free to experiment with other programs but for this assigmnet we require that you use VMD and Pymol.

The Assignment

  1. Learn to download structure files. Some structure files are often provided with the viewer programs for demonstration purposes, but you should download the structures of different proteins from the PDB.

  2. Learn to use Two Different Molecule Viewing Programs (Pymol and VMD).

  3. Choose Two Protein Structures (of Two Different Proteins).

  4. Use the programs to generate illustrations of interesting aspects of the structure of these proteins.

  5. Use the program of your choice to make a simulation movie.

  6. Make a Web Page!

  7. How you will be graded:

Problems? Questions about the Page or the Class? Contact the instructor