PostScript viewer

In addition to the text output, a postscript file is produced, which is a high quality drawing of the secondary structure (Figure 12.1). Since a line with the sequence name was included in the input file marry, seq the postscript file is named marry-ss. ps instead of the default name rna.ps. Postscript files can be printed on any postscript-capable printer or viewed onscreen using a postscript viewer such as gv or gsview. 

Figure 31. Spectral Outputs from Molecular Sophe (a) Bruker s XeprView (or Xepr if available), (b) Gnuplot, (c) Image plot (portable network graphics xxx.png ), (d) Ghostview (postscript viewer), and (e) Open Inventor Viewer (ivview) (see next page).

Molden can display molecular geometries in a variety of formats, including lines, tubes, ball and stick, ribbons, and CPK. The user has some control over colors and sizes. Molden also has features designed for the display of proteins and crystal structures. The display can be exported as postscript, VRML, Povray, and image files. It can also be configured as a chemical mime viewer. 

In the previously described example we see that the pair (4,70) has no inconsistent sequences, is predicted with probability 1, and occurs as a CG pair in one sequence, a GC pair in another, and a GU pair in the third. The AliDot. pi utility uses this information to display a dot plot equivalent to the postscript version. The viewer has better zoom capabilities than most postscript previewers and shows additional information, but requires the Perl Tk module to be installed. 

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