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.