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Re: [modeller_usage] Modelling Query

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

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage