This is the standalone version of SPServer (http://sbi.upf.edu/spserver), a web server to assess the quality of protein folds and protein-protein interactions using knowledge-based potentials (also known as statistical potentials).
python SPServerFold.py -f <PDB_PATH> -p <POT_TYPE> -o <OUT_PATH> -x <XML_NAME>
-f: Input file with the PDB proteins. It can be a PDB/CIF file, a list of paths to PDB/CIF files or a TAR.GZ/ZIP.
-p: Definition of atom-atom minimum distance. It can be CB or MIN.
-o: Output directory.
-x: Name of the XML output file (without the complete path and extension).
Example:
python SPServerFold.py
-f 1ivo.pdb
-p CB
-o ./output
-x 1ivo
python SPServerPPI.py -i <INPUT_FILE> -r <CHAIN_RECEPTOR> -l <CHAIN_LIGAND> -s <PPI_SOURCE> -o <OUTPUT_PATH> -j <JOB_ID> -p <POT_TYPE>
-i: Input file with the structures of the interactions. It can be a PDB/CIF file, a list of paths to PDB/CIF files or a TAR.GZ/ZIP.
-r: Receptor chain ID. Only necessary if a PDB/CIF file has been introduced.
-l: Ligand chain ID. Only necessary if a PDB/CIF file has been introduced.
-s: Type of input. It can be "pdb_separated" (two PDB structures separated) or "pdb_together" (one PDB structure with 2 chains being the proteins that interact).
-o: Output directory.
-j: Job ID.
-p: Definition of atom-atom minimum distance. It can be CB or MIN.
-c: If the argument is introduced, it calculates the crashes between the interacting proteins.
Example:
python SPServerPPI.py
-i BAX_BID_reference.pdb
-r A
-l C
-s pdb_together
-o ./output
-j BAX_BID_reference
-p CB
-c
