PURPOSE: This protocol is an example of how one can read in a series of protein files (either PDB, MOL2, MSV or DSV), clean the protein chains, optionally remove waters and write the cleaned proteins to separate pdb files and the ligands to separate pdb files. The protocol also adds a CleanReport.html for each input file which describes what actions were taken on the protein to clean it.

DISCLAIMER: This custom protocol is compatible with Discovery Studio 2.5 and Pipeline Pilot server version 7.5.2 (SES). It is provided "as is" and is NOT supported by Accelrys nor is it warranted for any purpose whatsoever. The user assumes responsibility for any malfunctions or bugs.