Re: [modeller_usage] SA IN optimize.py

vidhya sankar wrote: > i would like to implement *simulated anealing* protocol in *optimize.py > http://optimize.py/ script*.along with default optimization

If by 'optimize.py' you mean the script given at http://salilab.org/modeller/9v2/manual/node250.html then implementing simulated annealing is simple - it's just several calls to md.optimize() at progressively lower temperatures.

If you mean for automodel model optimization, simulated annealing is already done. You can change the SA protocol by tweaking automodel.md_level; see http://salilab.org/modeller/9v2/manual/node46.html

Ben Webb, Modeller Caretaker