When I run the compare.py script, there's an error:
OError: pdbnam_____E> Filename for PDB code not found: 5a3y
Directories: ../atom_files
Extensions : ;.atm;.pdb;.ent;.cif;.crd
(Also tried prepending 'pdb', looking for .Z, .gz, .bz2, .7z, .xz,
and trying PDB-style subdirectories - e.g. ab for pdb1abc.ent)
I have downloaded the structure of 5a3y in the file format of 5a3y.pdb and I save it in the same directory as the compare.py script. What should I do to get the script run? Thank you.
Hello everyone,
I finally found the solution to this problem.
the script on compare.py is this:
env = Environ()
env.io.atom_files_directory = ['../atom_files']
My friend majoring in IT said that it might be of the slash sign (/) which will make the directory moves one folder back, and the atom_files is where the Modeller searches the PDB files. So, I tried copying the same PDB files and put it into a new folder named "atom_files" and move that folder into the folder one step back from the folder containing your script and files.
For example: if you save your files and script in "homology modeling" with this directory C:\Program Files (x86)\Modeller10.1\bin\homology modeling,
then, try to save the "atom_files" folder in folder 1 step back from the directory which is in the "bin" folder with this directory C:\Program Files (x86)\Modeller10.1\bin
so then your "atom_files" folder directory will be:
C:\Program Files (x86)\Modeller10.1\bin\atom_files
and not
C:\Program Files (x86)\Modeller10.1\bin\homology modeling\atom_files
Hope it works for you if you encounter the same problem as mine. Best Regards, Caroline
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