SplitPDB_Commandline

SplitPDB command line options

Run the following command to access the built-in help of splitpdb:

java -jar splitpdb.jar --help

Depending on the version you use, you will see something more or less similar to this:

splitpdb -- extract data on a specific model from NMR-data RCSB Protein Data Bank files.
[SPLITPDB] 
[SPLITPDB] USAGE: java -jar splitpdb.jar <infile> [OPTIONS]
[SPLITPDB]        java -jar splitpdb.jar --help
[SPLITPDB] valid OPTIONS are: 
[SPLITPDB] -h | --help              : show this help message and exit
[SPLITPDB] -a | --allow-overwrite   : overwrite the output file if it exists
[SPLITPDB] -o | --outfile <file>    : write output pdb file to <file> (instead of '<infile>.split')
[SPLITPDB] -m | --model   <mid>     : extract data on model with id <mid> (instead of model 1)
[SPLITPDB] 
[SPLITPDB] EXAMPLES: java -jar splitpdb.jar 1blr.pdb -a
[SPLITPDB]           java -jar splitpdb.jar 1blr.pdb -o /tmp/1st_mdl/1blr.pdb
[SPLITPDB]           java -jar splitpdb.jar 1blr.pdb --model 8 -o 1blr_M8.pdb
[SPLITPDB] 
[SPLITPDB] REQUIRED INPUT FILES: This program obviously requires the PDB file <infile>.
[SPLITPDB] 
[SPLITPDB] NOTE: -If the file does not contain any models, the output file is a copy of the input file.
[SPLITPDB]       -It is considered an error if a model that does not exist is specified explicitely (-m).
[SPLITPDB] 
[SPLITPDB] RETURN VALUES: 0 on success, 1 on error, 2 on success if the input file did not contain any models.

We suggest you read the documentation provided with the release for up-to-date information.