Changes and additions from ASTRAL 1.75 to 2.01:

* Renaming

ASTRAL 2.01 was previously released as ASTRAL 1.75A.  Depsite the
renaming, none of the data have changed.  The associated domain
classification (previously called SCOP 1.75A) is now named SCOPe 2.01.
All files with "scopdom" in the name have been changed to "scopedom."


* Website

ASTRAL data are now part of the SCOPe website.  To keep the look
and feel familiar to current ASTRAL users, the tab called "ASTRAL
subsets" is organized in a way that's very similar to the old ASTRAL
website.  However, much ASTRAL data (for example, sequences and
PDB-style coordinates for each SCOPe domain) can also be accessed
directly from the SCOPe browser.

We will continue to update the user interface, even though the data
for a given release will remain stable.  One planned improvment will
be to allow downloads of additional derived data (e.g., sequence sets
and HMMs) for different clades in the tree, by clicking links next
to each clade in the SCOPe browser.


* SPACI and AEROSPACI scores

We re-calculated AEROSPACI and SPACI scores for all PDB files in
ASTRAL 2.01, including entries that were present in older versions.
New code tries multiple times to run PROCHECK and WHAT_CHECK, in
cases where those programs hang or crash the first time.  We also
obtain resolution and R-factor data using the XML data files from
the PDB; this should be more robust than trying to parse it ourselves
from text headers.


* ASTEROIDS

We are calculating ASTEROIDS using all protein chains from PDB entries
that are not classified in SCOPe 2.01.  This includes entries released
before the SCOPe freeze date that were not classified in SCOPe, as well
as entries released after the freeze date.  Nucleic acid chains are
not included in ASTEROIDS.

As described in the "Help" tab of the website, ASTEROIDS that meet all
of our reliability criteria will be promoted to SCOPe domains and
released as part of SCOPe 2.02, and in weekly updates to 2.02 after
that.  We have not yet determined how best to release ASTEROIDS that
do not meet these stringent standards for accuracy--they will not be
included in SCOPe until manually curated, but may be made available
upon request.