Dear Bin, 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, 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..... i dont know where i am making the mistake??? 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??? please help me understanding the scripts and the generated files to have good view of a good model. Thanking in advance. Muhammad Noon
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