Splitting a Macro-molecular Complex Efficiently and Flexibly

A program that splits components of a protein structure, returning separate ligand, protein-complex, waters, and other molecules. This version uses the low-level API to fragment and then combine selected components.

An example command that limits the protein-complex output to just the binding site residues would be:

prompt> python splitmolcomplexlowlevel.py -separateresidues input.pdb output.oeb.gz

Help is available for all the supported OESplitMolComplexOptions parameters:

prompt> python splitmolcomplexlowlevel.py --help all

splitmolcomplexlowlevel <inmol> [<outmol>]
Complete parameter list
    Display options :
      -verbose : If true, show molecule titles and number of binding sites

    SplitMolComplex options :
      -bindingsitenum : Select this binding site
      -covalentbondtreatment : Covalent bond treatment
      -covalentcofactor : Split covalent cofactors
      -covalentligand : Split covalent ligands
      -ligandfilter : Ligand filter category
      -ligandname : Ligand name
      -maxsitedistance : Maximum distance to be associated with the binding site
      -maxsurfacedistance : Maximum distance to be associated with the protein
                            surface
      -modelnum : Select this NMR model number
      -proteinfilter : Protein filter category
      -separateresidues : Separate individual residues before selection
      -surfacewaters : Select surface waters
      -waterfilter : Water filter category

    input/output options :
      -in : Input molecule (usually a pdb file)
      -out : Output molecule (usually an oeb)