A sample protocol to run DS MODELER with Python script (through either DS client or Pipeline Pilot client).

Input Parameters:
Align_File: sequence alignment file (.pir)
Known_Template: 3D template file (.pdb)
Python_Script: modeler python script file (modeler.py)
Mod_Bat: batch file to run MODELER (HwMod.bat)
Temp_Directory: a temporary directory (instead of default \$(RunDirectory))

All sample input files are provided. Please modify attached HwMod.bat to match the user’s own system for the first time, including, the working directory (should be the same as Temp_Directory), the machine name, and the local path of DS MODELER engine.

[Note] This sample protocol only works on Windows with DS client/server on the same machine. If it is run through PP, please block pipelines 1, 4,5,6 in the original protocol.

Thanks, Hongwei