POSTSTAMP

There is something inherrently wrong with the way STAMP assigns equivalences within multiple alignments. It considers an average set of ${\rm C}_{\alpha}$ coordinates and uses an average set of probabilities to derive equivalences when more than two structures are involved, and as a consequence, it appears to go wrong (sometimes only) during this process. Usually this is only when very distantly related proteins are being considered. A fix to this problem is to consider each pair of structures within the alignment separately, and to re-calculate the raw Rossmann and Argos probabilities. One need then define positions as structurally equivalent when all pairs of structures have a P_ij value larger than a cutoff at a particular residue position.

For example, for ten structures, there are ( $10 \times 9/2) = 45$ pairs. For a position to be structurally equivalent across all members of the family, P_ij should be $\geq 0.5$ for all 45 pairs.

POSTSTAMP does just this. It adds two new STAMP format fields to a STAMP alignment file: one tells whether the above is true (1) or false (0) for each position (i.e. is each position structurally equivalent across all members of the family); the second tells how many pairwise comparison have P_ij greater than or equal to the cutoff (e.g. 0.5).

For example,

poststamp -f globin.5 -min 0.5

Creates a file globin.5.post, containing the above data for a P_ij value of 0.5.