The University of Arizona
Macromolecular Crystallography Core Facility home page

UNIX Systems (django, gilmour, methylase)

A tutorial of unix commands

Where to find things

executables are in /usr/local/bin or /usr/freeware/bin

How to set up your environment

If you use tcsh or csh as your shell, most environmental variables expected by crystallographic packages are set for you. Exceptions are:
To run phenix, first type setupphenix
To run EMAN, first type setupeman

Printing

komeda (HP4000N LaserJet in 526) is the default printer
Choosing print from an application will send output to komeda
To print postscript or text files use the command
lp -d komeda file.name

Remote login

login access is restricted to local network. Let me know whether vpn works. I will not allow access from aol, earthlink, cox, etc.
you can only use secure applications (ssh, sftp or scp), you can not telnet or rlogin

X-windows access

From an xterminal (mac, linux), use the command ssh -Y yourname@django.biochem.arizona.edu VNC, a freeware x-windows server has been installed. Clients are available for both Windows and Macintosh systems (also UNIX/LINUX).
To run VNC,
a) Start the server on the computer you wish to log into: type vncserver You'll be given a screen number, n.
b) Start the client (vnc) on your pc or mac. Connect to computername.biochem.arizona.edu:n
c) When finished, log out. To kill the server with the command: vncserver -kill :n
It is not necessary to kill the server after each use. You can use the same screen number day after day. Please do not run multiple VNC servers.

You will need to restart the vncserver after a computer reboot.

Text Editors

Choose your favorite: Only vi and ex run on non-X capable terminals.
jot - a GL based WYSIWYG editor. Only available on SGI consoles
vi - old, standard UNIX editor.
Nedit - X-windows based text editor
xedit - another X-windows editor.
ex, ed, edit - don't ask - very old line-based editors, but they're still there

Submitting Jobs to run at a later time

Do not remain logged into the console while running long (more than 15 minutes) computational jobs. Detach the jobs from the terminal and log out. Other users may log you out if they've reserved the terminal and you are nowhere to be found.

Suspending and Killing jobs on UNIX systems

A process that is hung, or a computational job that is not doing what you wanted can be stopped with the command kill. Only the owner or superuser can kill a job. Determine the PID of the process, either with ps or top, then use the command
kill -9 pid
Kill can also be used to send other signals to jobs. One set of useful signals is STOP and CONT. STOP will suspend execution of a job until a CONT signal is given. The job is not killed, but picks up where it left off after the CONT signal is given. Again, you need to determine the PID of the job. Then
kill -STOP pid            will suspend the job, and
kill -CONT pid            will restart it.