Cool Hunk wrote: > I am a new Modeller user, i am having some problems running Modeller, > while i run the script using command "*mod9v7 model.py*" it doesnt run > completely and generates errors

What errors? We can only help if you tell us what the errors are.

> but when i run the script using command > *"Python model.py" *it runs completely and generate all the pdb files of > models but not the log file for it even though i have included the > function "*log.verbose()"* in the script, and the same is the case for > model evaluation script and energies calculation script.....

Python doesn't generate log files - the output comes out on standard output (i.e. your screen, if you didn't direct it somewhere else). To get something very similar to running mod9v7, use something like

python model.py > model.log

> my other question is about the model evaluation, that do i have to run > the evaluation script for each model individually and the compare the > final dope scores or the scripts takes all the models at once and give > me the final good model???

You can do it either way. You can evaluate a single model with the script at http://salilab.org/modeller/9v7/manual/node242.html Alternatively you can have automodel assess every model it builds automatically by setting assess_methods; an example is at http://salilab.org/modeller/9v7/manual/node20.html

Ben Webb, Modeller Caretaker