Secondary structure assignments in the file ss.txt are calculated from the experimental coordinates using DSSP
(W. Kabsch, C.Sander (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded
and geometrical features Biopolymers 22:2577-637).
An 'X' in the sequence indicates a residue of unknown identity.
A blank in the ss.txt file stands for a loop or other irregular structure.
The codes used in the ss.txt file are:
The file ss_dis.txt includes notation of regions that have not been experimentally observed in
addition to the secondary structure.
Here, X's indicate differences between residues that exist in the originally studied molecule (the
SEQRES records of the PDB file) but not in the observed structure (the coordinate records of the PDB file).
REMARK 465 in the PDB format file also lists discrepancies between the SEQRES and the coordinate section.
Format descriptions are available from wwpdb.org.
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.