On 3/24/10 9:57 AM, Anna Marabotti wrote: > thank you for your comments. You are true, on my machine I have Python > 3.0.1. However, Modeller seems to work in any case, since I was able to > model a protein with the automodel procedure sometime ago. Moreover, > yesterday I found a way to use the wiki script mutate_model.py: I started > from the launch screen of Modeller and typed: > > mod9v7 mutate_model.py my_modelname my_respos my_resname my_chain> > my_log.log
Right - the mod9v7 binary includes a copy of Python 2.3 for your convenience, so it will work on machines that don't have Python installed. But (unlike Python itself) you can't "import" any non-Modeller Python modules in your Python scripts, other than the built-in 'sys' module.
> I finally obtained my mutants. I had a look at them and they seem to be > correct; the only strange things are: i.in the PDB file, the atoms of the > new sidechain introduced by the program do not have the B-factor (I don't > remember if this was true also previously)
Modeller uses B-factor to record the value of the scoring function. It is not really comparable with the crystallographic B-factor. So even if the new atoms had the B-factor, it wouldn't make a lot of sense.
> ii. mutate_model.py launched in > this way does not produce the my_log.log file, but the mutate_model.log > file.
Right - the mod9v7 script produces a .log file with the same name as your input Python file. If you want to name the file yourself, you can ask the script to use standard input and output and redirect them yourself:
mod9v7 - my_modelname my_respos my_resname my_chain < mutate_model.py > my_log.log
> Finally, a little suggestion: probably it would be better to rename the wiki > script in another way, since two MODELLER have the same name: the wiki > script mutate_model.py and the command mutate_model.py that inserts > mutation, but without the whole mutant sidechain optimization by conjugate > gradient and MD.
A good suggestion!
Ben Webb, Modeller Caretaker