Re: [modeller_usage] How to change directory path for atom files
To: khuram sb <>
Subject: Re: [modeller_usage] How to change directory path for atom files
From: Modeller Caretaker <>
Date: Tue, 11 Nov 2008 08:32:59 -0800
Cc: modeller_usage <>
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.
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 mail list: http://salilab.org/mailman/listinfo/modeller_usage