CHM 579 Assignment #1
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
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
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
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.
- PyMol is free to download and build as it is open source software. However, Purdue University provides all students
with a site license which allows for simple installation and execution. You can download it here:
Pymol version 2. You must also install the
site license while on campus as the link will not work otherwise.
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.
- VMD is under rapid development, so get the latest program from the
VMD Web Site.
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.
- This program is under heavy development and is not availible to the public, so this is a great oppertunity to experience
something avaible to only a handful of people.
- Due to the limited time students would have with the VR environment, this is an optional portion of the assignment.
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.
- 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
- Learn to use
Two Different Molecule Viewing Programs (Pymol and VMD).
- Learn to rotate and zoom in on different parts of the structure.
- Play with different structure representations.
- Learn how to select different molecules, protein chains, residues and atoms.
- Learn how to output the structures in different image formats.
Two Protein Structures (of Two Different Proteins).
- These should be structures that you download from the PDB, not ones that were supplied with the graphics programs.
- If you don't have the slightest idea what structures to choose, you can try the
Molecule of the Month..
- There are links to articles related to each structure in the database, and there is also important information within
the header section of the pdb file itself. Learn about the proteins and the other molecules in the structure files.
Use the programs to generate illustrations of interesting aspects of the structure of these proteins.
- You can export images from the programs themselves or capture images straight of the screen, as discussed the lecture.
Only submit compressed image file formats, like jpeg or gif. Tiff, pict and other raw formats generate massive files.
You should include images generated by both viewing programs in your submission.
- Each image should illustrate some property of the protein's structure or function. We do not just want pretty pictures
- the biology needs to be there too! Some ideas:
- Show the architecture of the protein, secondary structure, packing, surface, fold, etc.
- Show some examples of interactions that stabilize the structure.
- If your pdb file has other molecules besides the protein in it, show them and how they interact with the protein.
What is the biological relevance of their presence?
- Is your protein oligomeric or part of a complex? How can that be clearly shown?
- Zoom in to clearly show interesting details.
- Show how the structure might affect the dynamics of the molecule.
- Use one or more images to show how the structure of the protein relates to its function.
Use the program of your choice to make a simulation movie.
- Many publications and conference speakers now include videoes of their simulations as part of the submissions, thus it is important to learn how
to make these publications to remain competitive.
- You must submit a video made in either PyMOL or VMD. The initial state of the system and the trajectory used to create the simulation will be
provided to you, all you need to do is make the movie.
- You may use either HTML5 or YouTube to post the video on your WebPage.
Make a Web Page!
- Include your images/illustrations with a
short explanation of the biological concept you are presenting.
- We are looking for a maximum of eight images on this assignment (preferably 4 from each program). Images beyond the first 8 will
not be graded. These do not include any additional images you will make for the Structural Refinement Server part
of the assignment.
How you will be graded:
- The assignment is worth 20 points.
- Provide images generated by Pymol and VMD (MINT is optional, but encouraged).
- Provide images of two different protein structures.
- Demonstrate the ability to show different aspects of the structures by rendering the molecules in different ways.
- Include a short, clear description of the biological idea conveyed in each image and answer/explanations to all
questions asked in the assignment.
Problems? Questions about the Page or the Class?
Contact the instructor