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.