meaning of "env.io.atom_files_directory"
Hi everyone,
I am working on the tutorial in http://salilab.org/modeller/wiki/Missing%20residues. I have my pdb files in C:\Users\Sajeewa\Desktop\protease_project\modeller_practice directory. In the script to generate the model with all residues
# directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files']
should this be changed as
env.io.atom_files_directory = ['C:/Users/Sajeewa/Desktop/protease_project/modeller_practice'] ?
I don't understand what it means by
'.', '../atom_files'
Could you please explain?
Thank you
Sajeewa Dewage
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
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Sajeewa Pemasinghe