Hallo,
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. 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
The program ends without writing the .log file.
I used this script with the previous versions of Modeller, on the same PC, without any problem. It's the first time I use this script since I installed Mod9v7 on my PC, but I've already used Modeller 9v7 on the same PC without problems. Could anybody suggest me how to do?
Many thanks in advance and best regards Anna ____________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabotti@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
"If you think you are too small to make a difference, try sleeping with a mosquito"
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
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
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
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Modeller Caretaker