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 structures
See 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 ID
User 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]