UNIX Systems (django, bartok, gilmour, methylase )
A tutorial of unix commands
executables are in /usr/local/bin or /usr/freeware/bin except for packages with special setup (e.g. CCP4)
Most environmental variables are set in the system cshrc file.
Exceptions: to run phenix, type setupphenix; to use eman, type setup eman; to run norma, type setupnorma
If you use csh or tcsh as your shell, you should be able to run any installed software packages.
If you prefer bash, you will need to setup your own environment.If anything does not work, see me
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
login access is restricted to local network. See me if you need to get in from elsewhere. I will not allow access from aol, earthlink, cox, etc.
you can ssh, sftp or scp, you can not telnet or rlogin
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, but please do not run multiple VNC servers.
You will need to restart the vncserver after a computer reboot. To get a toolbox, either start it by typing toolbox & or alter your xstartup file in your.vnc directory.
User files on either django or bartok can be used on the other computer. If you can't find these files, see me.
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
Please do not run multiprocessor computational jobs during periods of probable graphics use 10 am - 10 pm).These jobs can be submitted to run later using at. Prepare a file (job.sh) containing the commands you wish to run.
Then submit it with the command:
at time < job.sh
where time is the time you want the job to start. This is a 24 hour clock, so 9 PM = 2100. Also useful are at now (job starts immediately) and at tomorrow (starts at midnight).
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.