Mensur Dlakic wrote: > I am interested in the last part of this statement, which is calling > external programs. Could you provide a working example of how to call > ProsaII and evaluate each model? As it is, I use ProsaII at the end of > each Modeller run, but it would be nice if GA341 and ProsaII scores > could be obtained in parallel for easier comparison.

I don't use ProsaII here, so can't give you a working script, but you'd write a function such as:

import os

def prosaII(mdl): """Returns the ProsaII score of the given model."""

# Write the current model to a PDB file, for ProsaII mdl.write(file='prosaII-input.pdb')

# (insert Python code here to generate a prosaII input file)

# Run prosaII with the generated input file and PDB os.system('prosaII prosaII-input.script')

# (insert Python code here to parse the prosaII output, and # put the score into the Python variable 'pscore')

# delete temporary files os.delete('prosaII-input.pdb') os.delete('prosaII-input.script')

# Return the score to Modeller return ('ProsaII score', pscore)

Then you would simply pass this 'prosaII' function to 'assess_methods' rather than (or as well as) the normal assess.GA341 or assess.DOPE.

The rest is left as an exercise for the reader. ;) I suggest that the completed script be put into the Modeller wiki at http://salilab.org/modeller/wiki/ so everybody can use it.

> could be obtained in parallel for easier comparison. Also, is there any > way to get perl scripts for stand-alone pG calculations? Some time ago > Andrej (or Roberto) told me that those scripts were too unrefined to be > shared, but maybe that has changed?

I don't know if these scripts are still available or usable - sorry.

Ben Webb, Modeller Caretaker