Hello Modeller 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'
At least I hope this is the answer.
Thanks, Steve
Not at all. The first notation, with the [] implies a list wih two elements: '.' (the current directory) and '../atom_files' (another directory).
Your second notation points to a different place!
You should use the first notation, I think the second is either deprecated or outdated.
What was the problem when you used the first?
João [ .. ] Rodrigues
(Blog) http://doeidoei.wordpress.com (MSN) always_asleep_@hotmail.com (Skype) rodrigues.jglm
On Mon, Nov 2, 2009 at 12:09 PM, Steve Seibold seibold@chemistry.msu.eduwrote:
> Hello Modeller > > 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' > > > > > > At least I hope this is the answer. > > > > Thanks, Steve > > > > > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >
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
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João Rodrigues -
Modeller Caretaker -
Steve Seibold