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: http://salilab.org/modeller/9v8/manual/node26.html
If your problem is something different (no asterisks in your PDB file) then please send me your input files so I can reproduce your problem.
Ben Webb, Modeller Caretaker