Preparing a Protein

A program that selects the highest occupancy alternate locations of a protein, adds hydrogens in orientations that make appropriate hydrogen bonds, and splits out the complex for the selected binding site (optionally separating the ligand from the protein complex). This is an initial prototype of a “protein prep” workflow.

An example command that splits out the ligand and limits water sampling is as follows:

prompt> python proteinprep.py -waterprocessing ignore input.pdb prot.oeb.gz lig.oeb.gz

Help is available for all the supported parameters:

prompt> python proteinprep.py --help all

proteinprep [-options] <inmol> [<outcplx> [<outlig>]]
Complete parameter list
    SplitMolComplex options :
      -bindingsitenum : Select this binding site
      -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 filename (must have 3D coordinates)
      -cplxout : Output complex filename
      -ligout : Output ligand filename

    Calculation options :
      -alts : Alternate location atom handling (affects atom:atom interactions)
      -placehydrogens : If false, hydrogens will not be added
      -waterprocessing : How waters are processed (can greatly affect runtime)
      -standardizehyd : If false, bonds for hydrogens are not adjusted to standard
                      lengths
      -clashcutoff : Van der Waals overlap (in Angstroms) defined to be a bad
                     clash
      -flipbias : Scale factor for the bias against flipping sidechains such as
                  HIS

    Display options :
      -verbose : Display more information about the process