If a file name is specified input is read from that file, otherwise from standard input. With -out onesec secondary structure abbreviations are printed along with the sequence. Using these options a sequence file can be generated from a PDB file but it is also possible to get an abbreviated sequence string from a sequence file, e.g., as shown in the examples below.
Further options are available to include secondary structure information in the sequence file.
If -dssp is specified the secondary structure is taken from DSSP output. With the other option -2ndpred a list of files containing output from common automated secondary structure prediction programs can be provided. If more than file is given a consensus prediction will be determined from all predictions.