THE SGI SCREAM-SAVER

Chemistry Department, Indiana University, Spring 1996

This newsletter is available at the beginning of each month and covers the chemistry SGI cluster and the software available on it. If you want to subscribe, please contact the MolViz Facility Staff.

Items Covered in this Edition:

Chemistry on the Web

The Chemistry Department's web page is located at http://www.chem.indiana.edu. Many other web servers within the Chemistry Department can be reached from this web page:
Chemical Information Services from Indiana University
Chemistry Resources Center Web Server
IU Laboratory for Spectrochemistry
IU Molecular Structure Center
Internet Directory of Biotechnology Resources
Home pages of several research labs, which can be reached from the personnel/Faculty index.
Home pages of technical services, which can be reached from the Facilities index, including

the IU Molecular Visualization Facility Web Page:
http:/www.molvis.indiana.edu

Look for news and information about the Chemistry Department SGI network on this web page, including archives of past Scream Saver newsletters, UNIX guides and tutorials, and facility policies.

Web Browsers

Netscape version 1.1S for the SGI workstation, Mosaic version 2.2, and Lynx version 2.4 are available on all SGI workstations. Type netscape, mosaic, or lynx in a UNIX window to start. Lynx is a text-based browser with no graphics. Most users prefer Netscape over Mosaic for graphics-based Web browsing.

Netscape has several important menus listed at the top of the Netscape window. The bookmarks menu allows you to add the http address of the current web page that you are viewing to a list in the bookmark menu. You can quickly return to that web page at any time by returning to the bookmark menu and clicking on your saved address.

The Options menu allows you to toggle the display of several features in your Netscape window. The Options/Preferences submenu allows you to change many attributes of Netscape. If Netscape shows you error messages when you first start the program, make sure that these preferences are set correctly for your home directory on your workstation.

window and link styles
your home page location (the page that is first displayed when you start the program)
fonts
mail and news
news server = 129.79.1.20
RC directory should be your home directory ($HOME)
cache and network
Disk cache directory should be your_home_directory/.netscape-cache/
Clear memory cache and Clear disk cache on a regular basis: Netscape saves many files and graphics in this cache. When you return to the same web page, Netscape accesses files and graphics in your cache instead of getting the same information again over the network (to save time). This cache can become very large as you access many pages. To save disk space, clear disk cache on a regular basis.
images and security
choose your favorite set of the listed preferences
applications and directories
telnet application = xterm -e telnet %h %p
TN3270 application = xterm -e tn3270 %h
Rlogin application = xterm rlogin %h
Rlogin with User = xterm rlogin %h -l %u
temp directory = /tmp
bookmark file = your_home_directory/.netscape-bookmark
helper applications
Mime configuration files:
Global types file = /usr/local/lib/netscape/mime.types
Personal Types file = your_home_directory/.mime.types
Global Mailcap File = /usr/local/lib/netscape/mailcap
Personal Mailcap File = your_home_directory/.mailcap
proxies
no proxy preferences need to be set for basic Netscape operation

Web Servers

If your research lab has a SGI workstation, the NCSA web server software can be installed and configured on this workstation. This server will then allow the world (or a restricted subset depending upon your security set-up) to view selected documents that you create and place in the proper directories. The software to create and serve clickable image maps and statistics about your web page can also be placed on your SGI workstation. You can also set up your server so that programs and applications can be run on your server via web browsers.

If your research lab does NOT have a SGI workstation, you can use UCS computing resources which serve information onto the web. You can also use a PC or Mac as a web server. Contact UCS for more information.

A NCSA web server on a SGI workstation consists of the following directories and files:

/usr/local/etc/httpd/
directory containing all server software
/usr/local/etc/httpd/httpd/
server program (called the "http daemon"). To start the server, type /usr/local/etc/httpd/httpd. This command should also be added to /etc/rc2.d/S99local so that your server restarts if you your SGI is rebooted.
/usr/local/httpd/htdocs
directory containing your HTML documents
index.html this html document is first displayed when a browser accesses http://your_SGI_name/ without specifying a particular file.
/usr/local/etc/httpd/logs directory containing server log files
access_log a list of each request by each browser for each document on your server
error_log a list of errors encountered by the server program
httpd.pid the "process ID number" of your server. To stop your server, type kill -9 `echo /usr/local/etc/httpd/logs/httpd.pid`
/usr/local/etc/httpd/conf
server configuration files
access.conf sets server security features; can restrict access from specific computers or to specific documents
your_home_dir/public_html
directory containing your personal web pages in your home directory. Your home page is accessible if web browsers access http://your_SGI_name/~your_account_name/
your_home_dir/public_html/index.html
this html document is first displayed when a browser accesses http://your_SGI_name/~your_account_name/ without specifying a particular file.
Several HTML (HyperText Markup Language) editor software packages are available. Most SGI workstations have WebMagic, a powerful sofware package that is easy to use. WebMagic is a word processor that also has options to add the features that constitute a web page (horizontal lines, tables, graphics, etc.). Adobe Page Mill is also a simple, robust editor for the Mac. Macros to convert Word or WordPerfect documents into HTML format also exist.

Perhaps the best method to learn about HTML documents is to "surf the web" and see how other people have developed their web pages. The View/Source menu in Netscape is invaluable for understanding how the syntax of HTML specifies features of the web page. Viewing other pages is also a good way to observe how graphics can be a very effective method to enhance information, but too many graphics ca be distracting and slow down the display of a page. Several texts and web pages are good resources for creating web documents:

Once you have established a web page for your chemistry department laboratory, group, or office, your web page can be listed on the Chemistry Department web page. Your web page must be professional and complete (no large areas "under construction"). Once these conditions are met, contact John Huffman (huffman@indiana.edu) about listing your page on the Department of Chemistry page.

Please also use the official title of our department, which is "Department of Chemistry", and is NOT "Chemistry Department" in any web page that will be listed on the Department of Chemistry web page.

Automounting Disks between SGI workstations

File systems (selected directories and files on a hard disk drive) on one SGI workstation can be shared, or "mounted", by other SGI workstations. The standard mounting method keeps the files mounted all of the time. This requires a perfect network and significant efforts by system administrators to maintain and guarantee that files are always mounted.

We are now in the process of implementing "automount" on all of the SGIs. "Automounting" will automatically mount files only when a user executes an application requiring the mounted file. When the application is finished, the system detects the inactivity and automatically unmounts the file system after a delay (currently 5 minutes). For example, users who have a home directory on a remote system can log onto an SGI workstation and their home directory will be automounted and immediately available. Automounting eliminates network traffic and system administration efforts when the SGI workstations are not being used, and it is a popular feature used in many SGI networks throughout the world.

Automounting causes several minor changes. Most importantly, the path name of home directories that exist on remote systems are prefaced with /ruser, and the path name of application directories that exist on remote systems are prefaced with /remote. For example, if Rachel has a home directory on CHEMVGX (/chemvgx/people/rachel) and she logs onto PCHEM01, her home directory on PCHEM01 is named /ruser/chemvgx/people/rachel. If Rachel starts InsightII (by typing InsightII) on PCHEM01, she accesses /remote/saturn3/model/biosym/950/bin/insightII, the copy of InsightII on our server SATURN.

Commands that access all file systems on the SGI workstation will access only file systems that are currently automounted. For example, df will only list file systems that have been used within 5 minutes. Since most people use these commands to access only file systems on which they are currently working (and are therefore automounted), this should not cause problems.

Displaying X-Windows on Remote Workstations

A security improvement was made during June 1995 to all SGI workstations. This security improvement prevents users at remote (X-window) computers from displaying their X-windows on your local SGI workstation. Unfortunately, this prevents you from displaying X-windows from another SGI workstation in the Department of Chemistry onto the SGI that you are using. The best way to avoid this problem (and other potential network problems) is to work directly on the SGI workstation that will run the program.

If you prefer to run a program from a remote SGI on your local SGI, you can re-establish this ability: first type xhost hostname, then telnet hostname, and then run your program. The X-windows will be generated using the CPU of the remote SGI, but the windows will be displayed on your monitor. Note that some programs are licensed so that running the program on one CPU in one SGI and displaying the windows on another SGI may not work. When you log out, the xhost display privilege is automatically removed.

Converting between different coordinate file types

Babel is a program that converts many different coordinate files to other formats. For more information, type babel in a UNIX window to display information about the program. An excellent example showing the utility of babel is described below:

Our three most popular molecular modeling programs are InsightII, Cerius2, and PC-MODEL. Each of these programs can read coordinate files in Protein Data Bank (PDB) format. InsightII and Cerius2 also write files in PDB format. To write PC-MODEL structures in PDB format, follow Karl Scheidt's useful instructions:

  1. After structure is drawn in PC-MODEL, click WRITEF
  2. Save the structure as a SYBYL file type. SYBYL files usually end in ".mol", but this is not absolutely necessary.
  3. In a UNIX shell, type babel -imol SYBYL_file_name -op new_name.pdb
where SYBYL_file_name was the name you used in step 2. NOTE: the .pdb extension on the new name is not essential, but most programs will display these files in their automatic pop-up menus only if they have the .pdb extension. It is good practice to use the correct extension.

New Software

The new version of Biosym (v 95.0) is installed on the SGI network. Netscape version 2.0 will soon be available on all workstations. This version supports java applications. Type netscape to start. Adobe Acrobat Reader 2.1 will soon be installed on all SGI workstations. Felix version 95.0 is available, but not yet installed. Contact Marty if you want to install Felix v 95.0 and you have purchased a license for this software. The new version of Cerius2 (v 2.0) has just arrived, and it will be installed soon.
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Last updated: 01/23/2001