First, a big acknowledgement to Steve Searle (European Bioinformatics Institute)
for getting STAMP to run (finally) under OSF and 64 bit machines generally.
Also thanks to Andrew Torda
(Australian National University, Canberra), Dave Schuller (University of California-Irvine),
Mike Tennant (SmithKline Beecham Pharmaceuticals, Harlow, UK),
Asim Siddiqui (LMB, Oxford) G.P.S. Raghava (LMB, Oxford), and James Cuff (EBI)
for their help and various painstaking trawls through my spaghetti code.
Apart from bugs, etc., the noticable changes are:
1. STAMP now reads compressed PDB and DSSP files. It will also look for files that
are stored in a brookhaven style directory structure (e.g. distr/mb/pdb4mbn.ent).
2. Output is now flushed (fflush) during scanning. Purely a cosmetic thing for those who
want up to the minute output when the program is running.
3. AVESTRUC now has an option to calculate an average for all aligned positions. It also
now outputs values to the temperature factor fields in the PDB output to denote those
averaged positions corresponding to structurally equivalent regions (blue in RASMOL
colour by temperature) and those equivalenced fortuitously (red). It will also highlight
positions showing identical or conserved residue character.
4. PDBSEQ has some new options, including the ability to output separate files
for each domain, and now outputs a sensible description of the protein by
considering the TITLE, COMPND and SOURCE entries in each PDB file. Note that the
default format is now FASTA.
5. DSTAMP has been changed drammatically, and is now (I think) much more useful. The
input files for ALSCRIPT are now much prettier, including cylinders/arrows for helices/strands
and colouring/fonting according to residue property conservation within the sequence alignment.
It can also be used on alignments not derived using STAMP (i.e. from GCG, AMPS etc.).
6. STAMP now appears to run smoothly under OSF. Once again thanks to Steve Searle. Versions
have also been compiled and tested on IRIX, Solaris and Linux.
7. CLUS2BLC and SMSF2BLC have been replaced by a general alignment conversion program written
in PERL (ACONVERT). More details are given below. Note that this is a general alignment
conversion utility that might be useful in other contexts apart from STAMP.
8. The significance of sequence identity following structural alignment is now estimated
according to Murzin (1993), JMB, 230, 689-694.
9. Three new programs have been added to the package (see specific instructions below):
MERGETRANS allows one to combine transformations from a variety of different
sources (i.e. ALIGNFIT and STAMP). It either uses a user-specified identifier to link the
two files (i.e. one found in both files) or the first common identifier if none is specified.
MERGESTAMP. Like MERGETRANS this program permits one to merge
various kinds of STAMP data. However, it considers more than merely
the transformations, and attempts to combine the alignments as well.
It can be used in exactly the same way as MERGETRANS (i.e. to combine
files that contain only transformations), but will also attempt to merge
alignments in the file, if they are present. The alignments must be
in BLOCK format (see the depths of the manual for details, and for how
to convert things like Clustal or MSF into BLOCK format). MERGESTAMP
can combine files that do not contain transformations as well (i.e. those
that contain only alignments), and can thus be used for sequence data
handling as well.
EXTRANS allows one to select and extract particular domains from a transformation file.