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Re: [modeller_usage] "Structure not read in" error

Thank you for your feedback. I appreciate your help and also providing access to this freely available program. Basically I've been spending 5,6 hours today on setting up and running this program and got frustrated at some point. I looked at both the manual in the installed folders and online documentation. But it seems that I have to look more carefully since you mentioned my alignment is also not correct. I find all those colons at the second line of the PIR format alignment confusing, maybe it's just me! 
But anyways I keep trying.

Thanks again,
Omid K.



From: Modeller Caretaker <modeller-care@ucsf.edu>
To: Omid Khalouei <omid9dr18 AT hotmail.com>
CC: modeller_usage@listsrv.ucsf.edu
Subject: Re: [modeller_usage] "Structure not read in" error
Date: Thu, 23 Feb 2006 16:14:20 -0800

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. 

The directory is specified by setting the atom_files_directory variable.
See the simple example at http://salilab.org/modeller/manual/node23.html
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. 

	Ben Webb, Modeller Caretaker
--
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