We will be using some of these tools starting next week, so here we take some time to get familiar with some basics. For the most part, you can search using Google; I will try to provide some guidance and/or decent links here.
SHELLS
It is easy to find tutorials on shells. A somewhat generic one is here. Personally, I prefer the tcsh shell. However, this is not the default on OS X. If you would like to see how to change your default shell on OS X, directions are here. Here are a few links that I have found to be pretty good:
DOS/Windows shell tutorial
OS X/linux/bash shell tutorial
OS X/linux/tcsh shell tutorial
The main issue you might have with your shell is that the current directory "." or "./" is not in your path. (one way to refer to a file in the current working directory is ./filename). This is supposedly a security risk, but everyone I know puts "." in their path. To add "." to your path:
- bash: at prompt type "PATH=.:$PATH; export PATH" (or put this in your ~/.profile file)
- tcsh: at prompt type "setenv PATH ".:$PATH" (or put this in your ~/.tcshrc file)
To set this permanently, check tutorial sections on modifying the startup file(s).
Windows
This course is not really set up to work well with Windows machines. That being said, this Lifehacker post on terminal software is useful:
The Best Terminal Emulator for Windows
EDITORS
For basic editing, you may use Simple Text. More ambitious users may wish to try vi (or vim) or emacs. You must be careful using Notepad and/or simple text, as we wish to keep the files ASCII/text files. Sometimes OS X would like to give these files different suffixes and/or change the file to some sort of formatted data, which is not good!
PLOTTING
Many of you have been using Excel to make graphs, however Excel is a poor choice for scientific plotting. First choice for new scientists would probably be Plot2, available at the App store or the website for free. Here is a short tutorial (under construction). There is another program called MagicPlot, which we are experimenting with.
My favorite program to use is Grace, but it requires the Macports UNIX layer. It is menu-driven, and after a short amount of time, you are able to make really nice data plots, as well as regression lines, in-place data manipulations and so on. Here is one tutorial. I use this program on OS X also, but installing it on OS X is somewhat convoluted.
FINALLY, if all these options either do not work for you, or you are finding yourself spending a lot of time (by "a lot", I mean more than 30 minutes), trying to get a plotting program to install/work, just use Excel.) Remember that Excel looks only at file extensions to tell what is in the file, so you may have to use ".txt" or ".csv" instead of ".dat" for you data files.
REMOTE ACCESS/SECURITY
VPN
Do not use the VPN application if you happen to be on campus and are using campus wireless or wired connection! You only have to use the VPN if you are off-campus, connecting through a third-party ISP.
Using a VPN on OSX is pretty easy. You should have received an email which includes a small file ("vpn-sw-student"). Open up System Preferences -> Network and click on the Add/"+" button.
Select the VPN Interface and click "OK". Now configure that interface.
Enter the server address (vpn,uop.edu) and your PacificNet ID. Now click on "Authentication Settings"
Use the instructions in the email to complete this part. When you are finished, click "OK" in the small pop-up, and "Apply" in the main window. Make sure "Show VPN status in menu bar" is checked. Close System Preferences. All you have to do to connect now is pull down the VPN menubar item and click "Connect". You will be prompted for your PacificNet password and be connected. This effectively puts you on Pacific's network, and will allow you to connect to the UNIX machines.
CONNECTION USING SSH
In order to access the on-campus OS X machines, you need to use ssh ("secure shell"). Once you have started up the VPN software and have logged in using your PacificNet password, you can use ssh.
OS X:
ssh is installed by default on linux and OS X machines. Open a terminal (a regular terminal, not a tkcon from VMD!); terminal is found in Applications -> Utilities. Continue below.
Windows:
Use PuTTY (find it here). PuTTY's documentation. You will need at least putty.exe (for connecting remotely) and pscp.exe (for securely transferring files). Using PuTTY is fairly straight forward (but feel free to ask me if you need help!). Simply run "putty.exe" or "pscp.exe" from a DOS terminal.
Once you have a terminal open (whatever OS you use), the command is:
$ ssh user@target-machine
For example, when I need to ssh to one of my machines, I say
$ ssh mccallum@10.10.6.5
The first time, you will get some information about a new connection, and would you like to proceed? to which you should reply "y". After that, it asks you for your password, and you should be connected. This now is a shell on the remote machine, and you may proceed with Week 3 lessons.
FILE TRANSFER
Whether you want to send a pdb file TO the remote machine, or get one BACK from the remote machine, you will need to use 'scp'. scp stands for "secure copy". The general format of the command is
(sending)
$ scp local-file user@remote-machine:path
or (receiving)
$ scp user@remote-machine-IP:path/remote-file local-directory
It is generally easier to send from, and pull to your Mac. So, you may wish to have two terminals open: one which is connected to the remote machine, where you issue your commands and make new files, run jobs, etc. On the other, you can pull the files you have created back to your PC so you can plot data, load into VMD locally, etc.
Let's assume you have the file 1RSV.pdb in your home directory on a remote machine, and you wish to put it in your VMD directory on your PC. The command would be
$ scp user@remote-machine-IP:1RSV.pdb ./VMD
(Recall that "." means "current directory"; The colon after the machine IP represents your home directory in this case.) If you have the file trajectory.dat in your VMD/data/ directory on your PC, your current working directory was your home directory, and you want to put it in a directory called "Chem181" on the remote machine, the command would be
$ scp VMD/data/trajectory.dat user@remote-machine-IP:Chem181/
(For all of these commands, you will first get an authentication/fingerprint message—it is OK to acquiesce to this—then you will have to enter your remote password for each command.)
There are good GUI applications for OSX (Transmit is the one I have used).