Dear Ben, 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
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); ii. mutate_model.py launched in this way does not produce the my_log.log file, but the mutate_model.log file. In any case, Modeller seem to work properly even if Python 3.0 is installed. What do you think about? If you want, I can send you the mutate_model.log file
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.
Thank you very much and best regards. Anna
-----Messaggio originale----- Da: Modeller Caretaker [mailto:modeller-care@salilab.org] Inviato: martedì 23 marzo 2010 19.07 A: Anna Marabotti Cc: modeller_usage@salilab.org Oggetto: Re: [modeller_usage] error in using mutate_model
On 03/23/2010 06:06 AM, Anna Marabotti wrote: > I tried to model a mutant of a protein using the mutate_model.py script > available in the Wiki section of MODELLER site at: > http://www.salilab.org/modeller/wiki/Mutate%20model. Therefore, after > copying the script on a executable file, I opened the black window to > launch Modeller commands and typed, as suggested: > python mutate_model.py my_modelname my_respos my_resname my_chain > > my_log.log > but obtained the error: "python is not recognized as internal and/or > external command, or as an executable, or as a batch file" despite I > have Python installed on my PC.
It looks like you have a Windows machine. You probably need the full path for Python, e.g. on my machine it is C:\python26\python.exe
> I also tried to launch the command without "python" and typed: > mutate_model.py my_modelname my_respos my_resname my_chain > my_log.log > and this time the error was: > File "C:\Programmi\Modeller9v7\mutate_model.py", line 4, in <module> > from modeller import * > File "C:\Programmi\Modeller9v7\modlib\modeller__init__.py", line 69, in > <module> > import _modeller > ImportError: No module named _modeller
My best guess here would be that you have Python 3 installed on your machine. Python 3 is very different to Python 2; Modeller only works with Python 2.
Ben Webb, Modeller Caretaker