Optional Parameters

-append <bool>

Option to append to current loop dictonary 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.

-added_date <value>

Date the files were added to the DB 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 neccessary 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]

-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

[default = “loopdb”]

-log <logfile>

The argument for this flag specifies the name of the log file. This overrides any specified prefix.

-settings <settingsfile>

The argument for this flag specifies the name of the settings file. This overrides any specified prefix.

-verbose :

Triggers copious logging output

[default = false]