have problem running modeller 9.10
Hi,
I am trying to use modeller to model a chimera protein. I am going through the online tutorial and documentations. However I found that I cannot run modeller on my computer. I have a windows 7 machine with python 2.7 installed. The error message I got when I type mod9.10 model-default.py in command window is:
'import site' failed; use -v for traceback Cannot open logfile model-default.log: Permission denied.
I am in the same fold as the model-default.py file. Anyone know what is going on? Many many thanks.
On 12/3/11 4:30 PM, Yu Li wrote: > The error message I got when I type mod9.10 > model-default.py in command window is: > 'import site' failed; use -v for traceback
http://salilab.org/modeller/9.10/FAQ.html#19
> Cannot open logfile model-default.log: Permission denied.
See #6 at http://salilab.org/modeller/release.html#windows
Ben Webb, Modeller Caretaker
Hi,
I would like to Thank Ben for his quick respond. I turned off the UAC on my machine and it did not seem to help. I copy the whole folder under documents and now the program was able to run. However, I did not get the pdb file as output. The log file indicate an error occured:
pdbnam_____E> Filename for PDB code not found: 5fd1 Directories: .;../atom_files Extensions : ;.atm;.pdb;.ent;.crd (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, .7z, .xz, and trying PDB-style subdirectories - e.g. ab for pdb1abc.ent)
I am rather confused here since I expect the python code will be able to creat a file with the name indicated here and then write to it. Thanks for your help. On Sat, Dec 3, 2011 at 7:30 PM, Yu Li yuliyy@gmail.com wrote:
> Hi, > > I am trying to use modeller to model a chimera protein. I am going > through the online tutorial and documentations. However I found that I > cannot run modeller on my computer. I have a windows 7 machine with python > 2.7 installed. The error message I got when I type mod9.10 model-default.py > in command window is: > > 'import site' failed; use -v for traceback > Cannot open logfile model-default.log: Permission denied. > > I am in the same fold as the model-default.py file. Anyone know what is > going on? Many many thanks. > > > >
On 12/4/11 12:40 PM, Yu Li wrote: > I copy the whole folder > under documents and now the program was able to run. However, I did not > get the pdb file as output. The log file indicate an error occured:
This is obviously complaining that it can't find a PDB file for *input*, not that it can't write the output PDB:
> pdbnam_____E> Filename for PDB code not found: 5fd1 > Directories: .;../atom_files > Extensions : ;.atm;.pdb;.ent;.crd > (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, > .7z, .xz, > and trying PDB-style subdirectories - e.g. ab for > pdb1abc.ent)
Copy the 5fd1 PDB input file into the same folder as your example. Alternatively, copy the atom_files folder (you can find it in the Modeller examples folder) into the same folder that you copied the automodel folder into.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Yu Li