Changes and additions from ASTRAL 1.55 to 1.57: * Default sequence set Genetic domain sequences, first introduced in 1.55, are now the default sequence set in ASTRAL. Original-style sequences are also available. * Single sequence retrieval FASTA sequences for individual SCOP domains and PDB chains can be downloaded using a CGI script. The script can retrieve sequences derived from either SEQRES or ATOM records. For SCOP domains, the script can retrieve sequences in genetic domain style or original style. * PDB-style coordinate files for domains The ATOM records corresponding to each SCOP domain have been collated into PDB-style coordinate files. Header and remark records with more information about the domain are also provided. These files can be retrieved individually for particular domains via a CGI script, or downloaded in a single archive. * PDB chain sets A set of sequences derived from each PDB chain in ASTRAL (rather than each SCOP domain) is now included, as well as representative subsets selected at the 90% and 95% id levels. Files derived from PDB chain data (rather than SCOP domain data) all have names beginning with "astral-chain-". * Bibliographic entries Some SCOP domains are based on bibliographic PDB entries for which the coordinates are not available. The PDB code for these domains begins with '0'. These entries were previously excluded from ASTRAL. However, because SEQRES records (although not ATOM) are available for some bilbiographic entries, the sequences for these entries now appear in ASTRAL and in the RAF file. Because numbering of residues in the RAF file is normally based on the ATOM records, and the bibliographic PDB entries have no ATOM records, each residue in the RAF entries for bibliographic chains has been numbered starting at 1. * Other updates to RAF file The Rapid Access Format (RAF) file format has changed slightly from version 0.01 to 0.02. The PDB datestamp field now reflects the last modification time of the PDB file, rather than the date the file was obtained from the PDB. * AEROSPACI scores In previous releases of ASTRAL, representatives in selected subsets were chosen according to their SPACI score, a numeric score that provides some insight into the reliability and precision of a crystallographically-determined structure. However, some high- resolution PDB structures may not be the best representative for a given set, due to unusual (possibly engineered) properties of the protein. Representatives are now selected according to Aberrant Entry Re-Ordered (AERO) SPACI scores, which are SPACI scores with additional penalties subtracted for aberrant structures. In this release, aberrant structures were identified using Alexey Murzin's comments on each PDB chain. PDB chains with comments including one or more of the following keywords were penalized by lowering their AEROSPACI score by 2.0: chimer circular disorder error incorrect interrupted misfolded missing mistraced mutant permut truncat Also, theoretical structures (which are not present in SCOP or ASTRAL domains, but still assigned SPACI and AEROSPACI scores) receive an additional 5.0 penalty to their AEROSPACI score. * 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 this release, we also translate modified residues in cases where the base amino acid is clearly identified in comments in the PDB file. At this time, the change only affects PDB entries updated since the last release of ASTRAL. However, all entries will be re-examined for a future release. A list of the affected PDB chains, along with residue identifiers, 3-letter codes, one-letter codes, and comments, follows: 1C9PA 115 IAS N # modified residue 1E33P 69 FGL C # post-translational modification 1E5XA 309 MSO M # modified residue 1E5XB 309 MSO M # modified residue 1E79D 199 GLH E # modified residue 1FW3A 144 S1H S # modified residue 1FW3B 144 S1H S # modified residue 1HBMA 400 MGN Q # modified residue 1HBMD 400 MGN Q # modified residue 1HBNA 400 MGN Q # modified residue 1HBND 400 MGN Q # modified residue 1HBOA 400 MGN Q # modified residue 1HBOD 400 MGN Q # modified residue 1HBUA 400 MGN Q # modified residue 1HBUD 400 MGN Q # modified residue 1HQ6B 82 PVL S # modified residue 1HQ6D 82 PVL S # modified residue 1HYVA 130 CAF C # modified residue 1HYVA 65 CAF C # modified residue 1HYZA 130 CAF C # modified residue 1HYZA 65 CAF C # modified residue 1I45A 168 FTR W # modified residue 1I45B 168 FTR W # modified residue 1I83A 384 CAS C # modified residue 1I83B 384 CAS C # modified residue 1IAVA 221 SEB S # modified residue 1IECA 132 SEB S # modified residue 1IECB 432 SEB S # modified residue 1J97A 11 BFD D # modified residue 1J97B 511 BFD D # modified residue 1JBEA 75 SNN D # modified residue 1JBEA 76 ACY G # modified residue 1JL0A 68 SEG S # modified residue 1JL0B 68 SEG S # modified residue 1JQ6A 87 CAS C # modified residue