Re: [modeller_usage] meaning of "env.io.atom_files_directory"

[Modeller Caretaker <>]

On 9/21/12 11:30 PM, Sajeewa Pemasinghe wrote:
> should this be changed as
> env.io.atom_files_directory  = ['C:/Users/Sajeewa/Desktop/protease_project/modeller_practice']?

That would probably work, although strictly speaking the directory 
separator on Windows machines is \, not /, so you want

env.io.atom_files_directory = 
[r'C:\Users\Sajeewa\Desktop\protease_project\modeller_practice']

Note the leading 'r' to tell Python this is a 'raw' string. Otherwise 
the \ character has a special meaning:
http://docs.python.org/tutorial/introduction.html#strings

> I don't understand what it means by
>
> '.','../atom_files'

It tells Modeller to look in the '.' and '../atom_files' directories for 
PDB files. '.' and '..' are the standard names for the current directory 
and the parent directory, respectively (not Modeller specific).

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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