Permission denied message
Dear Ben, I am beginner in modeling of proteins. I downloaded the Modeller 9v7 (Windows package) and I am following the tutorials. I just started the Basic Modeling tutorial, but when I type any command at the command line, for example: mod9v7 build_profile.py, the following message appear:
Cannot open logfile build_profile.log: Permission denied
I also tried to run the command: mod9v7 model.py. and I got the same message. I downloaded all input and output files for this tutorial. So, what should I do?
P.S.: the list of systems that I am using: Windows Vista, Modeller 9v7 and Phython 2.3.5
Thanks so much,
Manoel
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Manoel Arcisio-Miranda wrote: > I am beginner in modeling of proteins. I downloaded the Modeller 9v7 > (Windows package) and I am following the tutorials. I just started the > Basic Modeling tutorial, but when I type any command at the command > line, for example: mod9v7 build_profile.py, the following message appear: > > Cannot open logfile build_profile.log: Permission denied
See step 6 at http://salilab.org/modeller/9v7/release.html#windows
Windows Vista has stricter security than older versions of Windows; it won't let you write into a directory that you don't own, so it won't let Modeller create log files there (or any other output files, such as models). Make a new directory, put the files there, use the 'cd' command to change into it, and then run 'mod9v7'. Don't run things directly out of the Modeller install directory.
Ben Webb, Modeller Caretaker
Dear Ben,
thanks for the information. I did it, but another problem started.
I moved the Modeller9v7 folder to Desktop and now when I tried to run the command mod9v7, the following message appears:
'mod9v7' is not recognized as an internal or external command, operable program or batch file.
I also tried to move Python 26 in the same folder. However, it stops to work. In addition, when Python is in Program files folder and I try to run some example from Modeller (for example: salign_multiple.py) using IDLE, I got the following message:
Import Error: no module named modeller
So, what should I do? I'm sorry, but I'm really confused how to use Modeller in the Windows Vista platform.
Thanks so much,
Manoel
________________________________ De: Modeller Caretaker modeller-care@salilab.org Para: Manoel Arcisio-Miranda manoelarcisio@yahoo.com.br Cc: modeller_usage@salilab.org Enviadas: Seg, Outubro 26, 2009 1:24:31 PM Assunto: Re: [modeller_usage] Permission denied message
Manoel Arcisio-Miranda wrote: > I am beginner in modeling of proteins. I downloaded the Modeller 9v7 (Windows package) and I am following the tutorials. I just started the Basic Modeling tutorial, but when I type any command at the command line, for example: mod9v7 build_profile.py, the following message appear: > > Cannot open logfile build_profile.log: Permission denied
See step 6 at http://salilab.org/modeller/9v7/release.html#windows
Windows Vista has stricter security than older versions of Windows; it won't let you write into a directory that you don't own, so it won't let Modeller create log files there (or any other output files, such as models). Make a new directory, put the files there, use the 'cd' command to change into it, and then run 'mod9v7'. Don't run things directly out of the Modeller install directory.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
________________________________ Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - Música - Esportes
____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com
Manoel, I have recently started using modeller and also have Vista. I created a folder under my username and put all my script and atom etc. files in it. I left the modeller9v7 folder in the program files directory it was installed into. I run modeller from the start menu and use the cd command to change to the directory with my script files. This setup has been working for me.
Justin
Quoting "Manoel Arcisio-Miranda" manoelarcisio@yahoo.com.br:
> Dear Ben, > > thanks for the information. > I did it, but another problem started. > > I moved the Modeller9v7 folder to Desktop and now when I tried to run > the command mod9v7, the following message appears: > > 'mod9v7' is not recognized as an internal or external command, > operable program or batch file. > > I also tried to move Python 26 in the same folder. However, it stops > to work. In addition, when Python is in Program files folder and I > try to run some example from Modeller (for example: > salign_multiple.py) using IDLE, I got the following message: > > Import Error: no module named modeller > > So, what should I do? I'm sorry, but I'm really confused how to use > Modeller in the Windows Vista platform. > > Thanks so much, > > Manoel > > > > > > > ________________________________ > De: Modeller Caretaker modeller-care@salilab.org > Para: Manoel Arcisio-Miranda manoelarcisio@yahoo.com.br > Cc: modeller_usage@salilab.org > Enviadas: Seg, Outubro 26, 2009 1:24:31 PM > Assunto: Re: [modeller_usage] Permission denied message > > Manoel Arcisio-Miranda wrote: >> I am beginner in modeling of proteins. I downloaded the Modeller 9v7 >> (Windows package) and I am following the tutorials. I just started >> the Basic Modeling tutorial, but when I type any command at the >> command line, for example: mod9v7 build_profile.py, the following >> message appear: >> >> Cannot open logfile build_profile.log: Permission denied > > See step 6 at http://salilab.org/modeller/9v7/release.html#windows > > Windows Vista has stricter security than older versions of Windows; > it won't let you write into a directory that you don't own, so it > won't let Modeller create log files there (or any other output files, > such as models). Make a new directory, put the files there, use the > 'cd' command to change into it, and then run 'mod9v7'. Don't run > things directly out of the Modeller install directory. > > Ben Webb, Modeller Caretaker > -- modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > ________________________________ > Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 - > Celebridades - Música - Esportes > > > > ____________________________________________________________________________________ > Veja quais são os assuntos do momento no Yahoo! +Buscados > http://br.maisbuscados.yahoo.com
Manoel Arcisio-Miranda wrote: > ********Dear Ben, > thanks for the information. > I did it, but another problem started. > > I moved the Modeller9v7 folder to Desktop
No, don't do that! That will (as you discovered) break Modeller. (In fact, this is the case for most Windows programs - don't move them after you install them.) Make a new directory for your own scripts, but leave Modeller (and Python) where they are. If you want to run the Modeller examples, copy (not move) the examples directory (not the whole Modeller directory) to a new location.
Ben Webb, Modeller Caretaker
participants (3)
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beauch46＠msu.edu -
Manoel Arcisio-Miranda -
Modeller Caretaker