Linux and the X-ray Lab Computer

1. Linux is an operating system for PC's It is used in place of Windows It is free, versatile, and flexible It is a bit harder to do system maintenance on but much more powerful. Linux and the X-ray Lab Computer

2. Linux vs Windows • Linux is case sensitive--abc, Abc and ABC are all different. In Windows they are identical • We will be using Linux mainly in the command line mode while Windows is used in graphical mode • Linux does graphics with Xwindows while Windows uses mainly DirectX

3. Accessing the Xray Computer from a computer lab terminal. • A method of sending text data between the computers. We will use Secure Shell (ssh) which encrypts data during transmission. ssh is built into Linux but special software must be used on Windows • An Xwindows server must be running on the Windows machine if graphics are to be done. • The ssh server must be configured to pass Xwindows commands on ssh.

4. Logging on to the X-ray Lab • Start → All programs →Standard Software →Telecommunications • Select pc-xware • There should be a icon for an x screen in the lower right • This is the Xwindows server and required for all graphical programs.

5. Go back a window and click on Secure CRT • Secure CRT • File → New Session(3rd icon top left) • Next • Hostname: “kpccd2.chem.purdue.edu” • Username: “chm696” • Next • Session name: kpccd2 • Enter the connect window (upper left) • Right click on kpccd2 and select properties • Under x-windows select pass through • This will be the default. Do not do again

6. Connect Login (PASSWORD on the board) The program will remember the session kpccd2 and the settings. Enter xclock to make sure things are working. You should see a clock on the screen.

7. Linux Directories • It is important the terminal is set to the correct directory. Each structure has its own directory and each student will need to create and use his own directory. • The home directory for this course is /home/chm696. Note Linux directory levels are separated by / (not \ line Windows). • When you log in you will automatically be in this home directory.

8. Changing Directories • The command is cd (lower case) followed by the directory name. • The name can either be full or relative. • Full name cd /home/chm696/mydirectory • If you are in /home/chm696 then only enter cd mydirectory. • Directories can have many sub directories such as /home/chm696/mydirectory/structure1 • Data for homework or structures to be worked on will frequently be left in the home directory

9. Making your directory • The command for making a directory is mkdir • To make your directory in /home/chm696 a. Make sure you are in /home/chm696 (entering cd with no directory always moves you to the home directory. b. Enter mkdir mylastname(all lowercase) c. cd mylastnameto go to your directory

10. Files may be referred to by their full name which includes the directory /home/ccd/somefile or if the default is the correct directory just the file name To find out what is in your directory a. enter ls for a listing b. enter ls -l for a complete listing including file size and access date Working with files

11. To rename or move a file enter mv file newfile. If newfile has a different directory in the name then the file will be moved to that directory. To copy a file enter cp file newfile To remove a file enter rm file. Be careful as once removeded files cannot be recovered!

12. Most programs are run by simply entering the name of the program if it is known To find out whether a program is known and where it is located use which program To run an unknown program enter the full file name of the program Running Programs