- Right click your desktop and open a terminal window, run
- cp ~dxu/.bashrc ~
- source ~/.bashrc
- This sets up your environment variables so that you can launch all the lab software properly.
- Get yourself familiar with Linux text editor "nano", just type "nano your_filename". Note that you cannot use mouse inside nano. If you prefer slow GUI editor, type "gedit filename".
- By the end of week one, you should know how to use the following commands:
- ls or llt (list files and folders, llt sorts everything by time so that last modified file will appear last)
- pwd (check where you are)
- cd (change dir)
- mkdir (make dir)
- rm (remove a file or folder)
- cp (copy)
- mv (move)
- cp -s (create a symbolic link instead of copying the actual file/folder)
- ssh (secure shell remote access to all lab computers, even from home, ask Matt how)
- scp or lcp (transfer files between computers, say savor and allspice)
- nano (or gedit)
- evince (open pdf files)
- nohup (no hangup, keep your jobs running even after you logout)
- You will be quizzed on these basic commands frequently.
- VMD (Visual Molecular Dynamics) is the most popular molecular visualization program, it is used to make most of the stunning figures and movies in our research. You will spend the first week going over 3 VMD tutorials. VMD has been installed in the lab. It's free, so you are encouraged to download and install it on your laptop or home computer from here
- The 3 tutorials you need to go over are VMD Molecular Graphics (Using VMD), VMD Images and Movies Tutorial, (the tutorial files are available at UIUC) and Using VMD with AMBER. Make sure to follow the online HTML version of the tutorials, the pdf version is reportedly missing some sections.
- Matthew and Dr. Smolin can show you how to download and set up the tutorial files in the lab.
- You are also encouraged to explore the tutorials for 2 other very popular molecular graphics program, they are also installed in the lab.
- Chimera Chimera tutorials
- Pymol Pymol Tutorial1 Pymol User Manual
At the end of the first week, you will be able to show off the pretty figures and movies you created from the tutorials, and you will be given a new molecule to apply the visualization techniques and create different representations and movies of the molecule. Here is an excellent example of VMD movie made by Andy Coombs.