The Purpose of the Scientific Computing Resource Center

The SCRC is designed to support the needs of two kinds of users:

  1. Those who have little or no experience in molecular modeling, but are willing to learn (by attending training sessions at NIH or elsewhere, and by reading the software manuals and other information) and perform their own work.

  2. Those who already have expertise in molecular modeling methods and software, but lack access to the specific hardware and software required for a project. Such users will benefit from the centralized collection of modeling software, hardware, and documentation available in the SCRC.

SCRC Computers

  1. Macintosh Quadra 950.
  2. Compaq 486.
  3. Silicon Graphics R4000 XS-24 Indigo.
  4. Silicon Graphics R4000 XZ Indigo.
  5. Silicon Graphics R4000 XZ Indigo.

SCRC Printers

Two color printers (Tektronix Phaser 200i and Phaser IISD) and a gray scale printer (Hewlett-Packard) are available in the SCRC for use in conjunction with scientific software. These printers can only be accessed from the computers in the SCRC. The commands for printing PS files are as follows:

Phaser 200i: lp -dcolor "file.ps"

PhaserIISD: lp -ddyesub "file.ps" (note: prints cost about $5.00)

HP SiMX (600 dpi): lp "file.ps"

Printer configurations vary, depending on the type of printer and its connection to your computer(s). Many printers at NIH are accessed through the campus or local networks. Printers are configured at the Unix level, and require expertise in computer system administration to do so.

Once configured, printing is an easy procedure. Common Unix commands for printing PS files include: lp "file.ps" or lpr "file.ps", depending on how your computer is configured. If you have access to multiple printers, you may use commands like lp -d "printer name" "file.ps" to select a particular machine (e.g. lp -dmy_printer molecule.ps). Type man lp or man lpr for further information about lp or lpr. You can also print directly from applications like showcase if your computer is configured to do so. You can transfer PS or EPS files to the Macintosh using a program like Fetch (a free program available on the DCRT PubNet server). PS or EPS files resident on a Macintosh can be input to a number of Macintosh graphics applications and printed from within those programs. PS files can be directly printed from the Macintosh using the LaserWriter Utility program available on the DCRT PubNet server ("Download PostScript File..." command of the "Utilities" menu).

Getting Started on SCRC Workstations

Three state-of-the-art Silicon Graphics Unix workstations equipped with molecular modeling software are currently available in the SCRC. A Unix workstation requires that you log into an account and store files in an assigned directory. An account named "modeling" has been created on both workstations for general use. You can obtain the password for this account from any of the SCRC staff. If you plan to use an SCRC workstation over the course of several days or weeks, a temporary personal account can be created by an SCRC staff member.

To log into a Silicon Graphics workstation, type modeling (or your assigned login name) in the login window and press the "return" key. Then type the account password. If nothing happens when you type from the keyboard, use the mouse to position the cursor inside of the login window. Once you are logged in, a window (called an "xwsh") is drawn on the screen. When you log in for the first time, type the command mkdir "your name" to create a directory in which to store your data files (e.g. mkdir john_smith). Do not include any blank spaces in the directory name. Next, type the command cd "directory name" to change to the directory that you have just created (e.g. cd john_smith). In future sessions, you need not use the "mkdir" command because your directory will already exist. Again, whenever you type from the keyboard, always use the mouse to position the cursor within the boundaries of the window that you are using.

You can run a particular program by typing its name (i.e. quanta to run QUANTA/CHARMm, sybyl to run SYBYL, and insightII to run Insight II/Discover) into the current window. Note the case sensitivity of the program names.

The pop-up menu named "Molecular Modeling" (upper left corner of the screen) lists all of the available molecular modeling software on the machine that you are using. To run a molecular modeling program using the pull-down menu, click on the "Molecular Modeling" menu, and while holding down the mouse button, move the cursor over the name of the desired program. Release the mouse button and a dialog box will appear requesting that you type in the name of the directory in which you want to work. When you are done, click on the "Accept" button. Next, the outline of the molecular modeling software window will appear. Click the right mouse button anywhere on the screen, and wait until the software is loaded. From that point on, you need not use additional Unix commands.

When you are finished, please exit from the modeling program and log out of the computer. To do so, position the cursor over the background area of the screen and press the right mouse button to display a new pop-up menu containing the "Log Out" command. Release the mouse button over the "Log Out" command.

Although SCRC workstations are periodically backed up, the safest approach to protecting your files is to make your own tape, and keep it in your possession. The SCRC will provide you with a blank tape upon request. If you do not create your own backup tape, there is a possibility that your files will disappear in time due to oversight, mechanical failure, etc.