Example Commands¶

The simplest way to run SPRUCE is by passing in an input biomolecular structure file (PDB or mmCIF) as the only argument.

prompt> spruce -in 3fly.pdb

Here, SPRUCE will correctly split and prepare 3fly.pdb with the -in parameter and the standard set of default options. The output will generally be a set of OEDesignUnit (.oedu) files, depending on the number of ligands and biological units in the asymmetric unit. In this case a single design unit file is produced (3FLY_A__DU__FLY_A-361.oedu).

There are also many options that can be invoked from SPRUCE on the command line. For instance, several options are available to help SPRUCE determine the ligand based on molecular features like the number of residues in a peptidic ligand:

So for example:

prompt> spruce -in 4obd.pdb -max_lig_residues 20

will correctly split and prepare 4obd.pdb, based on the -max_lig_residues which sets the maximum number of residues that can still be considered a ligand (required for larger, peptidic ligands like those in 4OBD).

Alternatively, one may want to prepare a biomolecular structure file based on the structure of a similar reference system. For instance, one may construct an OEDesignUnit with a set of site residues defined using a reference that includes a ligand:

prompt> spruce -ref 4OBD.oedu -in 1hhp.cif

Here, an mmCIF file (1hhp.cif) is prepared using the site defined in the output OEDesignUnit file prepared using the -ref option and an output .oedu file from the example above.

This could also have been done by specifying a site residue, for example (note the blank character for the insert code):

prompt> spruce -site_residue "ASP:25: :A" -in 1hhp.cif

To calculate the Iridium classification as a metric of structure quality, one must provide the map file that corresponds to experiment from which the biomolecular structure was derived:

prompt> spruce -map 3rox.mtz -in 3rox.pdb

Here a set of OEDesignUnit files will be produced from 3rox.pdb, where each oedu file will include its own Iridium score taken from a calculation on the density passed in through the -map option (3rox.mtz). The Iridium score can be extracted from any OEDesignUnit file using the spruce TK API, but it will also be reported in the spruce application’s output.

Several options in SPRUCE are available to help control how the system is prepared. For instance by default, spruce calculates partial charges and adds any hydrogen atoms missing from the experimental structure. However, if you have a have a downstream application that does not require certain time-consuming computations, like calculating partial charges or adding missing hydrogen atoms, you can tell SPRUCE to turn these features off:

prompt> spruce -protonate false -charge_radii false -in 3tpp.pdb

Here, SPRUCE will not add partial charges or hydrogen atoms to the output structures during the preparation process of 3tpp.pdb by using the boolean options -protonate and -charge_radii, both of which are set to true by default.

To prevent continually over-writing output files, the -prefix input parameter. allows you to give unique names to these files.

prompt> spruce -in 3fly.pdb -prefix FOO

will write the output structure into a file named FOO_3FLY_A__DU__FLY_A-361.oedu.

Finally, to help spruce identify ligands in the biomolecular structure file, use the -ligand_names flag as in this example with 3b3n.pdb.

prompt> spruce -ligand_names JI2 -in 3b3n.pdb