Re: [modeller_usage] Error in ini modeller-generated file
To: Felipe Villanelo <>
Subject: Re: [modeller_usage] Error in ini modeller-generated file
From: Modeller Caretaker <>
Date: Wed, 17 Nov 2010 11:46:24 -0800
Cc:
On 11/16/2010 07:34 AM, Felipe Villanelo wrote:
I'm trying of add some residues to an multimeric PDB, with a very simple
model script:
...
But after a short run, the program crash with tue following message:
...
_modeller.FileFormatError: read_pd_702E> File: modelo4-Al.ini, Line
2404 Could not parse data from file; file is probably corrupt.
Curiosily, the 'modelo4-Al.ini' file is generated by modeller during the
run, and I cannot bypass this problem
The alignment file is ok.
Maybe the problem is, that there is a ~40 Aa coil with no-template
sequence to model (between other ssequences with template)
I would need to see your input files to be 100% sure, but my best guess
is that if you look at line 2404 of that modelo4-Al.ini file, rather
than atom coordinates you will see asterisks (****). Because PDB is a
fixed-width format, any coordinates larger than 9999 (or smaller than
-999) cannot be represented, and probably what is happening is that your
very long insertion (which Modeller will initially generate as a simple
extended chain, since it has no additional information) ends up with
such large coordinates.
I suggest that you don't try to model that 40 aa region at all -
Modeller will not be able to generate a good model anyway.
I will fix this "properly" in a future release, but if you really want
to try to model that insertion, you can take that bad .ini file, put in
proper coordinates using a text editor (even replacing each *** with
zero coordinates would be an improvement, but sensible coordinates would
be best) and then rerun your script, using the 'inifile' keyword to
force use of your "fixed" initial model: