Steve Seibold wrote:
I believe I figured out the problem with the on-line tutorial. In the tutorial on-line in writes in the python script:env.io.atom_files_directory = ['.', '../atom_files'] However, I got it to work with only with: env.io.atom_files_directory = './:../atom_files'
You need a newer version of Modeller - at least 9v4. Older versions only understand the second syntax you show above, but newer versions will work with both. The second version is deprecated, however, just as João pointed out, because the colon (used here to separate two directories containing PDBs) is a valid character in directory names on Windows (e.g. C:\atom_files). Thus something like './:C:\\atom_files' would be ambiguous, whereas ['.', 'C:\\atom_files'] would not be.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage