Re: [modeller_usage] "Structure not read in" error
To: Omid Khalouei <>
Subject: Re: [modeller_usage] "Structure not read in" error
From: Modeller Caretaker <>
Date: Thu, 23 Feb 2006 16:14:20 -0800
Cc:
Omid Khalouei wrote:
I am just starting to use Modeller. Even though I have a major in
computer science, have used many bioinformatics tools, and am familiar
with Python, I haven't been able to figure out how to run this program.
To be honest I don't find it that user-friendly!
I suggest you first go through the basic modeling tutorial or at least
the first chapter of the manual on the website; your post strongly
suggests that you haven't done that. Constructive suggestions on how to
improve the documentation and program are, of course, welcomed.
Obviously there is always room to improve the user-friendliness of the
program, but in your case running a model-default-like script (you
didn't include yours, so I had to guess what you might be doing) gives
the following error in the logfile:
pdbnam__217W> Filename for PDB code not found: 1A8GA
Directories: ./:../atom_files
Extensions : :.atm:.pdb:.ent:.crd
This says that Modeller couldn't find a PDB file called '1A8GA' in
either the current directory or the ../atom_files directory, either as
is or with any of the 4 extensions listed. If this error message isn't
clear, let me know.
Basically I'm not sure in which folder I have to put my alignment and
PDB coordinate files.
This is the alignment file that I have created but
am not sure if it meets the specifications (they both refer to HIV-1
protease, residues 1 to 99 of chain A);
Your alignment file is also not correct. See the URL above for the
correct format.