Creating apo OEDesignUnits from a PDB file

Preparation of a biological structure file (PDB, mmCIF) to a fully charged, hydrogenated, molecular componentized object (design unit; DU; OEDesignUnit) is one of the more advanced functionalities offered through Spruce TK. This example shows how to construct apo DUs using an input PDB file and the OEMakeDesignUnits function.

Command Line Interface

This example uses an input PDB file, and will output a set of DUs from it to a temporary directory (see OEMakeDesignUnits for details on the API).

prompt> make_apo_design_units <input biomolecular PDB> <site_residue> [<electron density mtz>] [<LoopModelingTemplateDB>]


Download code and both the 1w50.pdb (the input PDB file), 1w50.mtz (the input MTZ file), and spruce_bace.loop_db (the input loopDB file)


prompt> 1w50.pdb "ASP:228: :A" 1w50.mtz  spruce_bace.loop_db

will generate the following output (failing to add partial charges to iodine):

DPI: 0.13, RFree: 0.28, Resolution: 1.75
Processing BU # 0 with title: BETA-SECRETASE 1, chains A
Found gap between ALA 157   A 1   and ALA 168   A 1  , with sequence GFPLNQSEVL
Opened database spruce_bace.loop_db
LoopDatabase Info:
    276 loops from RSCB last synced on 03-19-2020, were added to LoopTemplateDatabase on 03-19-2020 using Spruce Toolkit 1.0.0.a
    The loop database was built with a max loop length of 22, a termini crop length of 2, and excluding regular secondary structures
Warning: Failed to charge miscellaneous components
Warning: Unable to add partial charges and radii to DesignUnit: BETA-SECRETASE 1(A)__DU__biounit
Iridium Category: NA, DPI: 0.13, RFree: 0.28, Resolution: 1.75

See also