Insight II environment

User account:  There is currently no charge for using Insight.  One does have to create an account on the SGI.  A web-based form to create this account is found at (http://www.biochem.uthscsa.edu/apply/sgi.html).  Insight will be used in combination with file space on another computer named bioinf (where all accounts related to use of GCG, ultrascan, and other linux-based bioinformatics software are implemented).  If you already have an account on bioinf, it would be most convenient to make the SGI username and password the same.  If you do not already have an account on bioinf, one will be created for you with the same username and password as the SGI account.  You may change your password at any time by using the passwd command.

File system: When you log into the SGI, your starting directory will be your home directory on bioinf.  You may access it either by clicking the desktop folder with your user name on it, or by clicking <Desktop> in the Toolchest (upper right of the desktop) and selecting <Open Unix Shell>.  The path will be /home/user/<your username>.  You may make subdirectories as you wish to separate files generated by different tasks.  When you start insight, your user directory will be /home/user/<your username>.  If you wish insight to access files in a subdirectory, you should use the <session> <change_directory> command within insight to define the new user directory as /home/user/<yourusername>/<subdir>...  If you use a pilot tutorial within insight, it will change the user directory.  Upon returning to use your own data, you should use the <session><change_directory> to set your user directory back to /home/user/<your username> or /home/user/<your username>/<subdir>/.. as appropriate.

Starting InsightII: type insightII in a unix shell.

Remote access to InsightII: In principle, only SGI terminals are supposed to have adequate graphics support.  The program can be run from remote SGI terminals.  We have a floating license for one user at at time, so don't leave the program tied up unless you are actually using it.  You will notice that molecular rotation is slow in remote access mode.  This should improve as the university upgrades its internet routers.  From a remote SGI terminal, access insightII by the following steps:

• Log into bioinf for graphics access as follows: ssh -A -X -l <bioinf username> bioinf.uthscsa.edu
• From the bioinf window log through to the bioinformatics SGI by ssh -A -X -l <SGI username> node25
• In the node25 window type insightII
• The -l <username> part is only necessary if the username is different on the target computer.

Dialectical differences in the Unix bash shell:

The following link gives sources of general information about Unix and Linux.
This refers to commands typed at the unix command line.  Several versions of unix exist (called shells) differing by the syntax of a few of the commands.  The following is a short list of differences for those already accustomed to a different unix shell.

• Filename completion: When typing a command from the Unix bash command line, a partial filename will be automatically completed as far as uniquely possible from the files in the default directory if a <tab> is typed.  This replaces  <esc> for this purpose in some other Unix versions.
• Setting environment variables: If you are accustomed to using the setenv command, substitute export for setenv.

• To obtain files from databases, or other web sites, just access the site with Netscape and save the file.
• You may initiate ssh and scp sessions to exchange files with other computers upon which you have an account.
• You may access your bioinf directory with ssh and scp from external computers (including desktop PCs) to exchange files.
• If you use webmail, you can access it through Netscape and exchange files by e-mailing them to yourself or others as attachments.

• Open a Unix shell from the Toolchest
• telnet <your bioinf username>@node1
• Give your bioinf password.


This will give you access to the same bioinf user directory, and all command line programs available at bioinf within this window.

If you want to run a graphics programs on bioinf and view the results on the SGI:

• In a unix shell on the SGI type xhost node1
• In the bioinf command line window type export DISPLAY=node25:0.0
• Any graphics program started thereafter will show its display on the SGI terminal.


If you want to run programs normally started from icons on your bioinf desktop, like StarOffice, Acrobat, or GhostView:

• Complete the two steps above (logging to bioinf, and exporting your display to node25).  Then type kde.  This will give you the customary bioinf desktop with its icons all working properly.  You may notice that the same icons appear on the SGI desktop, but don't work from there.  You can reduce the size of the bioinf kde desktop by clicking the square in the upper right corner and dragging the corners of the kde window.  Running kde will change the background color of the SGI desktop, but not otherwise interfere with using insight.

• Help for vi.
• Type man edit to see a list of commands for edit.

• Left click on the edge (but not corner) of a window to raise it on top of all other windows.
• Right click on the edge and drag the mouse into the popup menu to lower a window (this will put it behind others that is may be obscuring).  This also works on iconified windows.
• Click the square in the upper right corner of the window to alternately make a window full screen or to return it to the size last specified by dragging the window corners.
• To iconify the window, click the small square just to the left of the one that toggles full size.
• To move a window, left click on the upper label bar and drag.
• To move an icon, left click on the icon name and drag.
• To activate an icon, left click on it other than on the name.
• To close a window, preferably look for a button that says something like <done> or <exit> or <cancel>.  In insight, <cancel> does not undo the previous operation; it just closes the window.  If there is no button to close a window, use the small horizontal bar in the upper left of the window.