khuram sb wrote: > I want to ask that when modeller directory (Work Station) is changed > from C directory (default) than how path of atom files is changed? > I want to know the whole procedure of changing directories and giving > the right path for atom files.

You can set env.io.atom_files_directory to a list of directories to search for PDB files. There are plenty of examples of this in the Modeller distribution. See for example the script file at http://salilab.org/modeller/9v5/manual/node13.html which searches both the current directory ('.') and the atom_files sibling directory ('../atom_files', one directory up from the current directory (..) and then back down into the atom_files directory). For example to search both 'C:\mypdb' and the current directory for PDB files use

env.io.atom_files_directory = ['.', 'C:\mypdb']

Note that in Python the backslash has special meaning so each one must be 'escaped' (basically, just use \ rather than ). Another way of writing this would be to use a Python 'raw' string (in which backslashes are treated normally and do not need to be escaped), e.g. r'C:\mypdb' rather than 'C:\mypdb'

See section 3.1.2 in the Python tutorial at http://www.python.org/doc/2.3.5/tut/node5.html for more details.

Note also that you will need to use Modeller 9v4 or later for this to work. In older versions, atom_files_directory is set differently.

Ben Webb, Modeller Caretaker