Here is a tutorial on basic output control.
Here is a list of common used output options.
-out:overwrite Ignore 'CHECKPOINT' file and the overwrite the PDB file(s).
[Boolean]
-out:nstruct Number of times to process each input PDB", default="1"
[Integer]
-out:prefix Prefix for output structure names, like old -series code",
Default="". [String]
-out:suffix Suffix for output structure names
Default="". [String]
-out:pdb_gz Compress (gzip) output pdbs", default="false". [Boolean]
-out:pdb Output PDBs", default="false". [Boolean]
-out:nooutput Surpress outputfiles. Default="false". [Boolean]
-out:output Force outputfiles. Default="false". [Boolean]
-out:show_accessed_options At the end of the run show options that has been accessed
Default="false". [Boolean]
-out:user_tag Add this tag to structure tags: e.g., a process id.
Default="". [String]
-out:no_nstruct_label Do not append _#### to tag for output structuresSee here for more info
-out:use_database Write out structures to database.
Specify database via -inout:dbms:database_name and wanted structures with
-in:file:tags [Boolean]
-out:database_filter Filter to use with database output. Arguments for filter follow filter name [StringVector]
-out:resume_batch Specify 1 or more batch ids to finish an incomplete protocol.
Only works with the DatabaseJobOutputter.
The new jobs will be generated under a new protocol and batch IDUser can dynamically, in run time specify command line options to mute/unmute specific/all channels and to change level of output.
-mute Mute specified chanels, specify 'all' to mute all chanels.
Defaule="false" [StringVector]
-unmute UnMute specified chanels. Default="false" [StringVector]Controlling Tracer output from command line. For Example:
# unmute all channels - default behavior, the same as just './a.out'
./a.out -unmute all
# mute all channels, unmute ChannelA and ChannelB
./a.out -mute all -unmute ChannelA ChannelB
# mute ChannelA and ChannelB
./a.out -mute ChannelA ChannelB
# Set priority of output messages to be between 0 and 10
./a.out -out:level 10
# disable output of channels names
./a.out -chname off-out:file:o Output file name. [String]
-out:file:silent Use silent file output, use filename after this flag.
Default="default.out" [String]
-out:file:scorefile Write a scorefile to the provided filename.
Default = "default.sc [String]
-out:file:fullatom Enable full-atom output of PDB or centroid structures.
Default = "false" [Boolean]-out:path:all All Files output Path. Default = '.' [Path]
-out:path:pdb PDB file output path. [Path]
-out:path:score Score file output path. [Path]
-inout:write_all_connect_info Writes explicit CONECT records in the PDB file,
for all bonded atoms, so that bonds are drawn for
anything that's bonded when the structure is viewed
in a program like PyMOL. (By default, only CONECT
records for noncanonical entities are written.)
Default = "false". [Boolean]
-inout:connect_info_cutoff Sets the threshold for writing CONECT records.
Bonded atoms separated by more than this
distance (in Angstroms) have a CONECT record
written. Set this to 0.0 to write all bonds.
Default = 0.0. [Real]
-inout:skip_connect_info Prevents the writing of CONECT records in the PDB file.
In the absence of this flag, CONECT records are written
for anything that isn't a canonical L-alpha amino acid or
a canonical nucleic acid. Default = "false". [Boolean]