Bevan & Brown Lab
Bevan & Brown Lab

Tutorials

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Tutorials Overview

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We currently post all of our tutorials on a public OSF page as a means for us to be  citable, open, and reproducible in our work (please cite!). The OSF is a series of tutorials provided to get an idea of the language and programs that we commonly use in our lab and to show you how we train our undergraduate research students. The more you work to learn the “how” and “why” of the programs now, the easier it will be when you utilize them for your own research. Understand what the command does and how you can utilize it; do not just type it in and move forward without understanding. This will greatly benefit you in the future. You must complete all tutorials before moving into your own research; however, this does not mean you cannot begin searching the literature about your project and briefly learning more while doing tutorials. These tutorials are provided under the assumption that you are a member of Bevan & Brown lab and are using a lab computer and/or Virginia Tech resources. HOWEVER, these tutorials are easily adapted to your own environment provided you have downloaded the software and installed some source code as in the instructions provided by them for your local environment. For example, most of these tutorials can be done remotely, on your personal computer, but will require download and installation, which is not always described here. We are not responsible for your ability to download other open-source programs. Finally, most tutorials are written under the assumption that these programs will be run using Unix/Linux. With some small tweaking of syntax, you will be able to use any operating system for these tutorials. As always, contact Dr. Brown (ambrown7@vt.edu) or Jonathan Briganti (jonbrig@vt.edu) if you run into any issues or need assistance.

Want to know even more about our research? Click on the Files button in OSF to see our usage files for GROMACS simulations and install instructions. We also have details on how we do docking on that page, some helpful papers, as well as a demo page for our PPAR project. Like how we organize things? Feel free to use this format for your own research projects and collaborations. Feel free to ask us any questions, we want work towards making our science more open and transparent. Happy Researching! 

Basic Tutorials for Getting Started in Our Group 

Unix/Linux tutorial

  • a. Go to this website and work through the tutorials. You will find it helpful to take notes or make a "cheat sheet" page in your notebook. Some commands like cd, mkdir, mv, rm, cp are essential commands you will use continuously. Know their overall usage. Take the final quiz, record your results in your notebook, and tell Dr. Brown your score.
  • b. You should now feel confident using a terminal and navigating around a computer using commands rather than clicking (because you can’t click on a supercomputer!). If you are not, take a look back at the tutorials until you feel like you could move around if you did not have a mouse.

VMD tutorial

  • a. All of our work is computational and we must show the readers and collaborators what we are doing on the screen in a clear, visual way. Learning how to visualize proteins and convey to the reader what we see and analyze on a computer screen is essential. VMD and PyMOL are two programs that will let you render images that will be descriptive and telling to your viewer.

  • b. Most protein structures we use come from the PDB. Go to the PDB (google it or type in rcsb.org). Look at the Getting Startedlink and explore the PDB to see what it can offer.

  • c. If you are working from your own computer - Download VMD. VMD will download onto Mac or PC. If you are on a lab computer, open VMD on your computer. To open VMD on a lab computer, open a terminal and type in “vmd”. The program should start. On the newer Mac computers, you will find VMD in the applications folder or on the launchbar.

  • d. Do the following VMD tutorial:

    • i. Do sections “Introduction” and “Working with a Single Molecule”.
    • ii. Click here for a helpful VMD cheat sheet .
    • iii. Generate an image for Dr. Brown and for your to put in your lab notebook.
    • iv. Take notes and record in your lab notebook. What key shortcuts do you need to remember? What are some tricks for making pretty pictures in VMD? Is there a cover image or figure in a journal article that looks nice? Try and replicate it. Your images of proteins should tell a story - think about that as you are learning the programs.

PyMOL tutorial

  • a. PyMOL is another visualization software. It makes much “prettier” images than VMD and is used for publication quality images. VMD and PyMOL work differently and can aid us in different ways, hence it is important to learn both.

  • b.You can download the educational version of PyMOL HERE. However, you can also get the full version by emailing Dr. Brown to provide the license info if you are a lab member. PyMOL is installed on all lab computers. PyMOL installs on Mac or PC. Open PyMOLon your computer. If you are on a lab linux computer - Open a terminal and type in “pymol”. The program should start.

  • c. Do the following tutorial exercises A to E.

  • d. This is a useful reference and there is a PyMOL reference on the restricted site.

  • e. View and take notes on the visualization lecture

  • f. Check out our new lab PyMOL tutorial here [Coming Soon].

  • g. With all of this in mind, make notes in your lab notebook and render one image for Dr. Brown too look at.

  • h. Are you feeling confident in your viz skills? Do you have some favorite colorings or tricks? Make sure to write down your steps any time you make images and realize you can change any feature in the "Edit All.." button.

GROMACS tutorial

  • a. GROMACS is the program we use to run molecular dynamics simulations. It is essential when doing this tutorial that you understand WHAT the command is doing, not just type it in to the next step. I highly suggest you write down the commands and what they do in your lab notebook. At any point in time, I need to to call back how you built a system with all details present.

  • b. Have a protein in solution? Need to equilibrate a protein before you do something else to it? Always start at the lysozyme in water tutorial. Do the lysozyme in water tutorial, write down what every command does after looking it up in the GROMACS user manual. Could you explain each step to me? Make sure you can!

  • c. Stop at energy minimization and put your energy graph in your notebook. Write a paragraph on what you THINK you did and how you did it. Schedule a meeting with Dr. Brown to discuss.

  • d. Have some down time? Read through Chapter 8 (page 245) of the Gromacs Manual to determine which analysis might be relevant, and how you could use the commands to perform analysis. Have you defined what your research question is yet? Start working on that now. What might you need to consider? Find analysis metrics that may be necessary or useful in answering your research question. This will be invaluable information as your project progresses.

Literature Search

a. Begin a literature search on your research topic. Pubmed is the best place to start. Ensure that you know how to use the library resources to access papers if needed (ask if you do not).

b. Find a lot of papers? How do you keep track of them all? Download EndNote from the VT website (it’s free) on your personal computer. This will be ESSENTIAL in your paper writing and reference tracking and makes life 1000x easier. It is much easier to install and learn it now, rather than later.

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