[modeller_usage] How to make Modeller run Iteratively

[Ashish Runthala <>]

Dear Modellers,
I am facing a small problem.
Just like command line arguments are there in scripts, is it possible to make MODELLER run iteratively, based on my defined set of parameters integrated with MODELLER. 
If so, how. I want to use Modeller in this way.

1. I want to call salign_iterative/align2d.py with varying proteins and dynamically considered constraints. 
2. Run align2d.py ( If salign is called, with my own set of defined parameters).
3. Run model_mult.py (Dynamically changing PDB template names with chainID with every run)
4. Iterate the loop 1-3 until some set of conditions are satisfied. 

How to make MODELLER functions change the considered parameters declared during the function call. 

Thanks
Ashish