Like DSTAMP, this program takes STAMP output and translates it in to input
for another program, namely Per Kraulis' program MOLSCRIPT. The program
allows one to create multiple molscript files (i.e. one for each structure
in the STAMP alignment file), or a single molscript file for an average
structure. Appropriate PDB files for these alternatives must be
generated by using TRANSFORM and AVESTRUC, respectively, prior to running
MOLSCRIPT.
When multiple structure are considered, structurally equivalent regions
(specified as for AVESTRUC) are shown as MOLSCRIPT helix, strand or coil.
Non-structurally equivalent regions are shown as 
trace. For an
example of how this looks, see Figure 1 [Russell & Barton, 1994] or Figure 1 in
[Russell, 1994].
The rest is up to you. Once MOLSCRIPT input files have been generated, they
can be modified to suit your particular display needs (i.e. using colour,
etc.).
The format is:
gstamp -f <STAMP alignment file> [ -c <STAMP char> -t <threshold> -w <window> -aligned -a -cons ]
-f, -c, -t, -w and -aligned is as for AVESTRUC and DSTAMP.
-a specifies that an average structure is to be used.
-cons specifies how the secondary structures are to be define in the
MOLSCRIPT files. By default, structures are displayed as helix or strand
only if all structures are helix or strand at the positions. `- cons'
means that structures are displayed as helix or strand if the majority
of structures are helix or strand at the positions. In both cases, the
remaining structures are drawn as `coil'.
BUG: sometimes GSTAMP will output single residue strands for Molscript
input. It is therefore necessary to modify the Molscript output to
correct the odd mistake (single residue strands produce funny pictures
in my version of MOLSCRIPT --- try it and see).