Usage
Please follow the following rules for a correct usage of the program:
The query protein must be located in the same directory of the PDBinder.py script as a PDB-formatted file.
The standard command for PDBinder is the following:
python PDBinder.py -i <PDB file>
Usage examples:
python PDBinder.py -i 1XYZ.pdb
The ouput files are the following:
predictions_<PDB file> : this file is a PDB-formatted file with the exception that the b-factor has been substitute with a flag value (1.000 for binding residue, 0.000 for non-binding residue) and in the last column is reported the propensity value as defined in PDBinder method (see References).
predictions_pv_<PDB file> : this file is a PDB-formatted file with the exception that the b-factor has been substitute with the propensity value as defined in PDBinder method (see References) and in the last column has been added a flag value (1.000 for binding residue, 0.000 for non-binding residue).
chimera_<PDB file>.com : this file contains a list of commands that can be read by UCSF Chimera in order to visualize the predictions made by PDBinder.
chimera_pv_<PDB file>.com : this file contains a list of commands that can be read by UCSF Chimera in order to visualize the propensity value mapped on the protein surface.
If you are using UCSF Chimera as molecular visualization tool, you can simply open the .com files provided by PDBinder with the predictions file in the same folder to quickly jump to view predictions on your query protein structure.