Spruce4Szmap

Overview

Spruce4Szmap is a utility program for preparing either a protein-ligand complex or separate protein and ligand files, into input ready for SZMAP or GamePlan. The input can be in PDB, MMCIF, or any fileformat that includes residue information (e.g. OEB). The ligand will be autodetected, but can also be specified on the command line if multiple potential ligands are present.

Example Commands

Prepare and convert PDB/MMCIF file 6FJT into szmap inputs

Prepares and converts PDB file 6FJT and outputs three files containing, the target, the ligand, and the solvent, respectively. It auto detects the ligand to be DKQ. Input could also have been MMCIF.

Input files

  • 6FJT.pdb.gz : PDB file to prepar

Command line

prompt> spruce4szmap 6FJT.pdb.gz

Output files

  • 6FJT_HIL__DU__DKQ_H-303_target.oeb.gz : The target
  • 6FJT_HIL__DU__DKQ_H-303_ligand.oeb.gz : The ligand DKQ
  • 6FJT_HIL__DU__DKQ_H-303_solvent.oeb.gz : The solvent

Command Line Help

A description of the command line interface can be obtained by executing Spruce4Szmap with the --help option.

> spruce4szmap --help

will generate the following output:

Help functions:
  spruce4szmap --help simple      : Get a list of simple parameters
  spruce4szmap --help all         : Get a complete list of parameters
  spruce4szmap --help defaults    : List the defaults for all parameters
  spruce4szmap --help <parameter> : Get detailed help on a parameter
  spruce4szmap --help html        : Create an html help file for this program
  spruce4szmap --help versions    : List the toolkits and versions used in the application
Complete parameter list
Input Options

-in : A molecule file to prep into szmap input(s) -map : input electron density map in MTZ format -max_lig_residues : Maximum number of residues to be detected as a ligand

Setup With Bound Ligand
-bound_ligand : Bound ligand molecule file, if not in input file
Setup With Ligand Residue
-ligand_names : Specifies the 3 letter codes identifying the ligands in
the structure
Receptor Options
-no_preparation : Option to not add hydrogens and build missing pieces -
if e.g. it is already prepared from elsewhere
Output
-prefix : Prefix of the szmap file(s).

Required Parameters

-in <filename>

Either a PDB or MMCIF file containing a protein-ligand complex or an apo protein. Any file format with residue information can be used (.e.g OEB); The structure will then be prepared with spruce and converted into a szmap usable input.

[keyless parameter 1]

Optional Parameters

Input Options

-map <filename>

A MTZ file containing the electron density map. This enables an evaluation of the Iridium category, and will also result in sorted structures based on the Iridium data.

-max_lig_residues

Maximum number of residues to be detected as a ligand, default is 5. Primarily needs to be set for larger peptidic ligands.

Output Options

-prefix <prefix>

Name of the output receptors files is based on the spruce design unit filename, this specifies the prefix for those filenames. The files are postfixed with the component type.

-log <logfile>

The argument for this flag specifies the name of the log file. This overrides any specified prefix. The default will be spruce4szmap_output.log, if no prefix is specified.

-settings <settingsfile>

The argument for this flag specifies the name of the settings file. This overrides any specified prefix. The default will be spruce4szmap_settings.param, if no prefix is specified.

Ligand Residue Options

-ligand_names
If spruce does not autodetect the ligand or multiple ligands are detected, this parameter can be used to assist in the ligand detection.
Form Example
<Residue Name> “LIG”
<Residue Name> “ALA-VAL-TYS-PHE-GLU”

Bound Ligand Options

-bound_ligand

Bound ligand molecule file if not in the input structure

Prepararation Options

-no_preparation [Default: false]

Flag can be set to true if input structure has been prepared elsewhere. If this flag is set to true the structure will no be prepared, meaning no hydrogens will be added, missing side-chains rebuilt, or chain breaks capped.