Pretty Structures via MOLSCRIPT

GSTAMP can be used to display the structurally equivalences found by STAMP. It works by creating an input file for MOLSCRIPT [18] (contact Per Kraulis to obtain a copy).

As for DSTAMP, a detailed description of parameters is given later. Here is a quick example, using the first globin alignment (i.e. containing only two structures).

First one needs to generate transformed PDB coordinates using the program TRANSFORM:

transform -f globin.5.clean

This will create 2 PDB files with coordinates superimposed: 2hhbb.pdb and 2hhba.pdb.

gstamp -f globin.5.clean

This reads in the six structures and the alignment and outputs six molscript files called (domain identifier).molscript.

One must then run molscript on each of these files that one wants to display. For illustration, we will run two very distantly related globins:

molscript < 1lh1.molscript > 1lh1.ps
molscript < 2hhba.molscript > 2hhba.ps

To give the two postscript files are shown in Figure 2.

Figure 2 Superimpositions of globin 1lh1 (left) and 2hhba (right).

By default, GSTAMP will show equivalent helix, strand and coil residues as MOLSCRIPT $\alpha$ helix, $\beta$ strand and coil, with un-equivalent regions being shown as ${\rm C}_{\alpha}$ trace.

At best, GSTAMP will give only a starting point for further refinement. Invariably, one will need to modify the orientation of the image for the best view, and probably need to tweak the assignments of helix and strand to look clear; MOLSCRIPT will not work, for example, if one has very short $\beta$ strands.