Optional Parameters
- -append <bool>
Option to append to current loop dictionary with additional structures, otherwise will fail if output DB exists
[Default=false]
- -title <title>
Title of the added structures, e.g. “Loops of aspartic acid protease structures”
[Default=LoopTemplateDatabase]
- -source_date <value>
Date the source was updated in the format MM-DD-YYYY. Defaults to today’s date.
- -ncpu <value>
Number of processors to run with, 0 means all available.
[Default=0]
- -max_length <value>
Max length of loops to add to the database. Note to add a buffer for necessary crop back in loop modeling
[Default=22]
- -crop_length <value>
Crop back this number of residues at the termini/breaks for each structure being evaluated
[Default=2]
See also
OESpruce::OELoopBuilderOptions::SetCropLength in the Spruce TK manual.
- -exclude_reg_ss <value>
Exclude sections with >75% regular secondary structures like helices and strand/sheets.
[Default=true]
- -prefix <prefix>
Prefix used to name output files, default is blank
- -log <logfile>
The argument for this flag specifies the name of the log file. This overrides any specified prefix.
- -settings_file <settingsfile>
The argument for this flag specifies the name of the settings file. This overrides any specified prefix. [Aliases=**-settings**]
- -skip_file <filename>
File containing PDB codes to skip, one code per line
- -verbose
Triggers copious logging output