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 -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage