We are looking into X-terminal emulators for NT machines, and information about those configurations will be added here when available.

What if my connection software can't do graphics?

Some terminal emulation software doesn't permit graphics output, or doesn't do a very good job. One example is a Mac running NCSA Telnet, which may produce poor-quality graphics that doesn't allow you to read the text or interpret the graphics. Other workstation/software configurations, while producing somewhat better graphics, are still not good enough for publication or for detailed examination of the output. You have a couple of options:

1. Avoid terminal graphics, and go directly to a plotter or printer. If you have a printer capable of postscript output, eps output, or plotter that accepts HP7550 plotter output, you can have the graphics output sent to a file, and then print that file. To do this, choose 'lwpost', 'EPSF' or 'HP7550' as the setplot option (depending on what kind of plotter/printer you have). After the program is run and has produced the output file, transfer that file to your computer and print it.

Note that the graphic output file will be overwritten each time you run a graphic output program. If you want to save the plot, rename the file!.

Sample session:

helix% setplot +----------------------> displaying all of 7 option(s) <---------------------+ |mactek Tektronix -- a Mac-Versaterm-Pro tektronix 4105 screen | |pctek Tektronix -- a tektronix 4014 screen [PC/Kermit] | |colorX Color X Windows Graphics Window | |monoX Monochrome X Windows Graphics Window | |lwpost to generate postscript for a Apple LaserWriter file ->gcgplot.ps | |EPSF to generate encapsulated popostscript file ->gcgplot.epsf | |HP7550 to select a HP7550 plotter file ->gcgplot.gl | | | | | | | | | | | +------------------------------------------------------------------------------+ Enter a command. Choices are: <up-arrow> and <down-arrow> scroll the list <return> makes GCG use the selected device Q quits without doing anything C creates and edits a new device (you can't delete from the site file) V views the selection (use C to edit a copy) Done Plotting Configuration set to: Language: psd Device: LASERWRITER Port or Queue: gcgplot.ps helix% mapplot MapPlot displays restriction sites graphically. If you don't have a plotter, MapPlot can write a text file that approximates the graph. Process set to plot with LASERWRITER attached to gcgplot.ps using the psd graphic interface. (Linear) MAPPLOT of what sequence ? a10852.gb_pat Begin (* 1 *) ? End (* 780 *) ? *** I read your enzyme data file "enzyme.dat"!! *** Select the enzymes: Type nothing or "*" to get all enzymes. Type "?" for help on which enzymes are available and how to select them. Enzyme(* * *): PostScript instructions for a LASERWRITER are now being sent to gcgplot.ps.

You can now bring the gcgplot.ps file back to your own machine using a file transfer program such as Fetch or FTP.

2. Use GCG's "Figure" option. Any Wisconsin Package graphics program run with -FIGure on the command line writes a source file of plotting instructions (called a figure file) that can be used as input to Figure. You then run 'setplot', choose that the output be sent to a file. Then run 'Figure' with the output file from your GCG graphics program. An advantage of making figure files from Wisconsin Package graphics programs is that you can store a graph and then replot it several times on different devices or make several copies of the same plot without having to redo an entire analysis.

Sample session:

helix% pepplot -fig PepPlot plots measures of protein secondary structure and hydrophobicity in parallel panels of the same plot. PEPPLOT of what protein sequence ? d44555.genpept Begin (* 1 *) ? End (* 413 *) ? The minimum density for a one-page plot is 359.1 residues/100 platen units. What density do you want (* 359.1 *) ? What Panels do you want to plot? a) Sequence b) Charged-polar-hydrophobic residue schematic c) Beta forming-breaking symbols d) Chou-Fasman Alpha-Beta prediction curves e) Alpha forming-breaking symbols f) Chou-Fasman NH2-end prediction curves g) Chou-Fasman CO2-end prediction curves h) Chou-Fasman Turn prediction curve i) Helical Hydrophobic Moment for Alpha and Beta j) Hydropathy and Hydrophilicity Please choose one or more (* ABCDEFGHIJ *): FIGURE instructions are now being written into pepplot.figure. helix% figure Figure makes figures and posters by drawing graphics and text together. You can include output from other GCG graphics programs as part of a figure. Process set to plot with LASERWRITER attached to gcgplot.ps using the psd graphic interface. FIGURE from what file ? pepplot.figure PostScript instructions for a LASERWRITER are now being sent to gcgplot.ps.

The file gcgplot.ps can be brought back to your own machine using a file transfer utility such as Fetch or FTP, and then printed to a postscript-compatible printer.

How can I modify a GCG graphics figure for publication?

There are a couple of alternatives:

• Save the graphic as a GCG Figure file. Most GCG programs that output graphics have a '-Figure' option, which will output the graphics into a .figure file. You can edit the figure file, and then use GCG's Figure program to convert it into a printable format such as postscript. Type 'genhelp figure' for more information, or see the sample session in What if my connection software can't do graphics?.
• If you have some knowledge of postscript, you can write the graphics output directly into a postscript file and edit that before printing. Postscript files are large and can be difficult to read, so this method is best used for minor modifications, such as scaling.
• If your Mac or PC has the EPSF editor, you can save the output as an EPSF file and use the EPSF editor to modify it.

How do I know if my setup can display GCG graphics?

For other configurations, look through the documentation to see if it can do Tektronix emulation.

If you don't see anything about Tek emulation, chances are that you can't display GCG graphics on your screen. If you don't want to purchase new connection software, you can still print out the graphics -- see the section on Printing in the FAQ.

What do I do with a figure file?

The main advantage of getting your output as a figure file is that you can edit the file if you really know what you're doing. You can scale, shift, and modify the graphics as you want, but you have to learn the options in the GCG figure command. It's not that hard, but if you want a simple output and are not interested in manipulating it, the figure output file is not much use to you. Instead, look at the Graphics section of this FAQ to see how to get the graphics displayed on your screen, or see How do I print GCG graphics to my postscript printer.

But suppose you already have a figure output file, and don't want to run the program again to get a different output? You can still use the GCG figure command to get your output into print or displayed on your screen. Type 'setplot', choose the appropriate option, and then run figure.

Sample session: printing a figure file

helix% setplot

+---------------------->  displaying all of 7 option(s)  <-------------------+
|mactek     Tektronix -- a Mac-Versaterm-Pro tektronix 4105 screen
|pctek      Tektronix -- a tektronix 4014 screen [PC/Kermit]
|colorX     Color X Windows Graphics Window
|monoX      Monochrome X Windows Graphics Window
|lwpost     to generate postscript for a Apple LaserWriter file ->gcgplot.ps
|EPSF       to generate encapsulated popostscript file ->gcgplot.epsf
|HP7550     to select a HP7550 plotter file ->gcgplot.gl
|                                                                            |
|                                                                            |
|                                                                            |
|                                                                            |
|                                                                            |
+----------------------------------------------------------------------------+
Enter a command. Choices are:
           and  scroll the list
           makes GCG use the selected device
          Q quits without doing anything

          C creates and edits a new device
          (you can't delete from the site file)
          V views the selection (use C to edit a copy)

Done

 
 Plotting Configuration set to: 
 
       Language: psd 
         Device: LASERWRITER
  Port or Queue: gcgplot.ps
233% figure 

Figure makes figures and posters by drawing graphics and text
together. You can include output from other GCG graphics programs as
part of a figure. 

  Process set to plot with LASERWRITER attached to gcgplot.ps
  using the psd graphic interface.

 FIGURE from what file ?  paupdisplay.figure

 PostScript instructions for a LASERWRITER are now being sent to gcgplot.ps.

Sample session: Displaying figure file on your screen

helix% setplot
+---------------------->  displaying all of 7 option(s)  <-------------------+
|mactek     Tektronix -- a Mac-Versaterm-Pro tektronix 4105 screen
|pctek      Tektronix -- a tektronix 4014 screen [PC/Kermit]
|colorX     Color X Windows Graphics Window
|monoX      Monochrome X Windows Graphics Window
|lwpost     to generate postscript for a Apple LaserWriter file ->gcgplot.ps
|EPSF       to generate encapsulated popostscript file ->gcgplot.epsf
|HP7550     to select a HP7550 plotter file ->gcgplot.gl
|                                                                            |
|                                                                            |
|                                                                            |
|                                                                            |
|                                                                            |
+----------------------------------------------------------------------------+
Enter a command. Choices are:
           and  scroll the list
           makes GCG use the selected device
          Q quits without doing anything

          C creates and edits a new device
          (you can't delete from the site file)
          V views the selection (use C to edit a copy)

Done
 
 Plotting Configuration set to: 
 
       Language: tekd 
         Device: VERSATERM-TEK4105
  Port or Queue: term

238% figure

Figure makes figures and posters by drawing graphics and text
together. You can include output from other GCG graphics programs as
part of a figure. 

  Process set to plot with VERSATERM-TEK4105 attached to term
  using the tekd graphic interface.

 FIGURE from what file ?  paupdisplay.figure

 When your VERSATERM-TEK4105 attached to tty is ready, press .
 
helix%