Hi,
I am using the Modeller Python interface to calculate secondary structure and surface accessibility for a number of PDB files. Whilst it works well for most PDBs, there is a crash in libmodeller.dll when using PDB 6G2J which cannot be caught by Python, i.e. the program simply exits with an AppCrash observed in the Windows Event Viewer.
My approach is to generate a completed PDB model using the modeller.scripts.complete_pdb function, followed by the model.write_data function method with ‘PSA’ and ‘SSM’ separately.
Please can you help me to resolve this issue? Let me know if you need any additional information to be able to reproduce the crash.
Thanks in advance,
Daniel
On 2/18/19 8:13 PM, dms305 wrote: > I am using the Modeller Python interface to calculate secondary > structure and surface accessibility for a number of PDB files. Whilst > it works well for most PDBs, there is a crash in libmodeller.dll when > using PDB 6G2J which cannot be caught by Python, i.e. the program > simply exits with an AppCrash observed in the Windows Event Viewer.
I would need to see your actual scripts and other inputs, as per https://salilab.org/modeller/9.21/manual/node10.html, and to know what version of Modeller and Windows you're using, in order to reproduce your problem.
Ben Webb, Modeller Caretaker
One thought: 6G2J.pdb is big, with 44 chains and 9175 residues. You might check to see if you're running out of memory.
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dms305 -
Jonathan Sheehan -
Modeller Caretaker