Structure alignment and analysis using BioJava
java -jar jce.jar --help
Non-option arguments:
[] [] ... []
Option Description
------ -----------
-?, -h, --help Show this help and exit
--CE, --ce Align with CE (default)
--Dali, --dali Align using DaliLite external binary
--FATCAT, --fatcat, --fc, --fcr Align with FATCAT - rigid
--FATCAT-FLEX, --fatcat-flex, --fcf Align with FATCAT_FLEX - flexible
--caonly [Boolean] Parse CA atoms only (default: true)
--chain Use first chain from ambiguous IDs
(default: first)
-d, --distances Generate distance matrix from list and
alignment files
-e, --extract Directory for extracted structures
-i, --info [Integer] Print structure information with
indicated verbosity (default: 0)
-l, --list Specify file of IDs for pairwise
alignments
--level Log4J log level (default: INFO)
-m, --multiple Multiple alignment
-n, --nproc Number of threads (default: 1)
-o, --outfile Output file
-p, --pdb Specify PDB directory
-r, --root Specify root for progressive alignment
--skip-pre Skip ID pre-processing
-z, --compress Compress generated structure files