Much has changed with STAMP. The changes are all described
in detail somewhere in this document. I list the major changes here:
1. STAMP programs now all accept command line arguments. Parameter files are no longer necessary, but one can still use them if prefered.
2. The scanning protocol has been improved; there are several new options, a new scoring system, and multiple means of sorting output.
3. Initial fitting via ROUGHFIT, and tree generation have been incorporated into the main program; the program MAKETREE is thus no longer needed, and is no longer included in the distribution.
4. Several new programs are now available in the package:
AVESTRUC --- creates an average model for a protein structural family given a STAMP alignment.
GSTAMP --- a program to create input for Kraulis' program Molscript, to display structurally similar/dissimilar regions within a family of aligned protein structures.
PICKFRAME --- allows the selection of a particular domain to be the `parent' in a superimposition (i.e. to have all other domains superimposed on top of it, leaving it un-transformed). This is very useful if you wish to combine, say, similarites involving separate domains from the same protein.
POSTSTAMP --- a method for reassessing STAMP alignments.
STAMP_CLEAN --- cleans up un-reliable regions (i.e. shortens long gaps where there is no structural similarity). This is most useful when one wishes to display or analyse an alignment.
VER2HOR --- converts the text alignment file output from STAMP to vertical format, for a quick analysis of the alignment (i.e. if you don't have ALSCRIPT)
CLUS2BLC, MSF2BLC --- two little programs to convert CLUSTAL or MSF format to the BLOCK format used within certain STAMP programs. Useful particularly if you don't have AMPS.
All of these are described in the sections that follow.
5. I hope that several bugs have been removed. As I have said before, STAMP was my first program, and I suspect that other bugs are still to be found. Thanks to all of those users who reported bugs, and I hope you keep reporting them. As ever, I shall swallow my pride.
This is the third version of STAMP to be distributed; comments are always greatly appreciated. STAMP was developed on a SUN SPARCstation and most recently modified using a Silicon Graphics INDY. As a consequence, it may suffer from system specific problems when running on other types of machines. Please let me know if you have such problems.