Re: [modeller_usage] "Structure not read in" error
To:
Subject: Re: [modeller_usage] "Structure not read in" error
From: "Omid Khalouei" <>
Date: Fri, 24 Feb 2006 01:18:45 +0000
Cc:
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 <>
To: Omid Khalouei <>
CC:
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.
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.