Guido Leoni wrote:
I have modeller8.1 on a windows machine. I try to use the model-segment.py script but modeller send me always the same error:forrtl: severe (64): input conversion error, unit -5, file Internal Fo
Assuming your template structure is PDB code 1daq, then you should check your initial generated model, 14521248.ini. You only have template information for a small part of the system, so Modeller can only guess the structure of the rest from the internal coordinates (it generates an extended chain conformation). This gives some of your atoms X coordinates of over 1000 angstroms, which cannot be represented in the PDB format (you'll see ******** instead). This is what is confusing Modeller; it's a limitation of the PDB format.
We will probably switch to using PDBML or MMCIF as the default coordinate output format in future releases of Modeller, which will solve this numbering problem, but even then, without template information, your model will be very poor. You should probably try to find a template to cover other parts of your sequence.
Ben Webb, Modeller Caretaker
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