GSTAMP

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 ${\rm C}_{\alpha}$ trace. For an example of how this looks, see Figure 1 [11] or Figure 1 in [12].

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).