Chapter 4-Graphics.

• The ability to toggle CPK for specified atoms using the specifier syntax which can be found in appendix 2.
• The ability to toggle atom color on the basis of specifiers.
  Available colors are:
  • red
  • blue
  • yellow
  • green
  • white
  • orange
  • cyan
  • magenta
  • grey
  • black
  • usr(this is a user defined color:see set usr-rgb)
• The ability to set atoms invisible.
• The ability to show the distances being monitored by dashed lines.
• The ability to set lines thick.

• PPM. PPM is a good standard graphics format that can be converted to any number of other formats using freely available programs. We now recommend using TIFF instead of PPM.
• Vector postscript.(EPS) This is suggested for the best quality wireframe
• Raster postscript.(EPS) This is suggested for situations where you don't anticipate modifying the image later with an external program.
• TIFF. TIFF is another raster format like PPM, but is 1/3 the size of PPM. This format is recommended if you anticipate processing the image with another program.

Demo

1. Create a 10 unit helix. This procedure is described in chapter 2.
2. Set the color of strand 1 to blue with the command:
   set col m1:1:*:* blue
3. Set the color of strand 2 to red with the command:
   set col m1:2:*:* red
4. Choose "CPK" from the Image menu, Choose it again to get wireframe back.
5. Selectively set the phosphate atoms on strand 1 to CPK by
   set space m1:1:*:P
6. Selectively set the phosphate atoms on strand 2 to CPK by
   set space m1:2:*:P
7. Write text by:
   • Determining the x,y position by clicking any mouse button over where you want the text to start.(example 200,500 )
   • Write "This is a test" at position 200, 500 by:
     set text 200 500 This is a test
     
8. Write this out as PPM with the command
   write ppm test.ppm