[modeller_usage] R: error in using mutate_model

[Anna Marabotti <>]

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:] 
Inviato: martedì 23 marzo 2010 19.07
A: Anna Marabotti
Cc: 
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
-- 
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage