GCG Graphics

Printing Graphic Files Created by GCG

A. Introduction
GCG is not a graphics-friendly program.

GCG originated as a mainframe program that was designed to work over a network via the least sophisticated possible dumb terminal.

Graphics support has been grafted on as an afterthought.

In order to work with graphics output, you must go through a certain amount of convolutions.

If you are working with NCSA Telnet, or a similar "barebones" terminal emulator program (Z-term, etc.).then there is no way to view graphics output directly.

You must either print it out as a Postscript file, or transfer the output file to your local desktop computer.

If you are working with VersaTerm Pro, you can view graphics using the Tektronics emulation.

If you are lucky enough to have an X-terminal or X-Windows emulation software on your computer (such as eXodus), then GCG's new SeqLab interface makes viewing graphics output utterly simple (however printing is just as challenging).

Working with graphical output in SeqLab will be discussed in the SeqLab tutorial.

B. Viewing graphical output with VersaTerm

Versaterm is a much more sophisticated method of communicating between a Mac and the Alpha than NCSA Telnet or other VT100 emulators.

However, to make full use of VersaTerm's ability to display graphical output, you need to configure GCG to produce output in a format that Versaterm can use. You will need to use the GCG command SETPLOT.

Type SETPLOT, this will bring up a window that looks like the figure below:

Use the C command to create a new device configuration for Versaterm. This will bring up a window that looks like the figure below:

Type E and then give your configuration a simple name, then use the TAB key to jump down to Description and again type in something that is meaningful to you.

Use the TAB key again to move down to Port/Queue/File and type in TERM.

[This is important]

TAB again to jump over to the Languages list, and use the arrow keys to select Tektronix.

TAB again and use the arrows to select Versaterm-TEK4105.

Now type M to return to the main menu and then type S to save your new graphics configuration. If you ever need to change to a different configuration (to save a Postscript file, for example), then you can use the shortcut command TEK at the $ prompt. Be sure to type in TERM when you are asked
To what port is your TEK4107 connected?

C. Printing GCG graphics output from the RCR Alpha

GCG programs that produce graphical output create files in a GCG proprietary format known as a .FIGURE file on the Alpha.

GCG has a program called (appropriately enough) FIGURE, that can translate the .FIGURE format into Postscript format, which can then be printed on any Postscript printer such as an Apple Laserwriter.

First you must set up your account on the RCR's Alpha to interpret GCG's graphics output.

Initialize GCG (just type "GCG" at the "$" prompt). Then type SETPLOT.

Choose your printer (usually the Apple Laserwriter is the best choice to receive Postscript output).

Next run a GCG program that generates graphical output - PILEUP is a good example, and direct the graphical output into a file named pileup.figure (or whatever name you prefer).

Next, type FIGURE and give the name of the figure file that you want to print.

FIGURE creates a file in your directory called PLOT.PS

Finally, print PLOT.PS to your favorite laserprinter using the PRINT command.

The PRINT command requires that you specify a "print que" (ie. a printer) as a destination.

Each lab will have its own favorite printer with a different print que name

The print command looks like this:
PRINT/QUE=RCR_TEMP PLOT.PS

That's it. Enjoy your beautiful printout.

D. Printing GCG graphics from a Macintosh computer

GCG has recently developed a Macintosh program called GCGFigure, which greatly simplifies viewing and printing graphical output files.

Rather than using the FIGURE program and going through a Postscript intermediate, GCGFigure allows you to view and print the .FIGURE format output files created by many GCG programs directly and also to save these files in the Mac friendly PICT format.

You can obtain the GCGFigure program by anonymous FTP to the RCR (mcrcr0.med.nyu.edu) or from the RCR's AppleShare server (Appletalk zone: NYU MC-Basic_Science, file server NYU MC-RCR) on the Apple Utilities volume in the MolBio folder.

Once you have created an output file from a GCG program, "pileup.figure" for example, it is necessary to transfer it to your Mac by FTP.

This is done most simply (and with the most confidence and control) with the Mac program Fetch.

I have a step by step tutorial on File Transfer on the RCR web site, but I'm not going to go over that material in this tutorial.

Once the file is on your Mac, launch the GCGFigure program, open the file and TaDa!!, you can see it, zoom in, scroll around, Print, and Save as a PICT.

Very neat, very simple, very nice. Certain files (such as the output from MAPPLOT are even in color! (But you are on your own to find a color Postscript printer.)

Using Computers for Molecular Biology
Stuart M. Brown, Ph.D., RCR, NYU Medical Center
Comments to: browns02@mcrcr.med.nyu.edu