Changes and additions from ASTRAL 1.57 to 1.59:

* PDB-style Coordinate Files for Domains

PDB-style coordinate files corresponding to each SCOP domain in
the first 7 SCOP classes were introduced in release 1.57.  Because
of the large size of the archive containing all these files,
smaller archives are now provided containing the most commonly
requested files:  those corresponding to the the 40% and 95%
identity genetic domain subsets.

* PDB Chain Sets

These were also introduced in version 1.57.  As of 1.59, a non-redundant
set (selected at the 100% sequence id level) is also available on
the "other sequences and subsets" page.

* New Subsets

Separate subsets are now available for the SCOP "dm" (Protein) level
and "sp" (Protein & Species) levels.

* Subset Selection Methodology

Because several users have asked for details on our subset selection
methodology (described in the 2000 paper), we now include verbose
logs showing which domains were selected as representatives, and which
other chains are part of the same subset.  The names of these files
are similar to names of other files containing selected subset data,
and contain the word -verbose-; they can be retrieved from our
web site in the same way as the other selected subset data.

* Sequences for SCOP classes 8 and above

The classification of proteins in SCOP classes 8 and above is described
by the SCOP authors as unreliable, and these classes are labeled on
the SCOP web pages as "not true classes".  However, because some
users need sequences for these classes also, the parent PDB chains
are now included in the RAF, and domain sequences are generated in
the same way as for SCOP classes 1-7.  These sequences are NOT
included in the full domain sequence sets or selected subsets, and
are only available from the "other sequences and subsets" page.

* Additional Residue Translations

Beginning with ASTRAL 1.55, chemically modified residues were
included in the translation table which maps the 3-letter codes
found in PDB files to one-letter codes in our sequences.  In version
1.57, we also began translating modified residues in cases where the
base amino acid is clearly identified in comments in the PDB file.
In this release, this methodology has been applied to all chains
in the RAF, including chains for which the PDB entry has not been
recently updated.  A list of the affected PDB chains, along
with residue identifiers, 3-letter codes, one-letter codes, and
comments, is now linked from the page describing RAF.