Flexible ligands Bug ?

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Flexible ligands Bug ?

Postby alesser » Tue Apr 06, 2010 5:06 am

I think I may have encountered a bug in PyRx ... when I try to make the residues in my macromolecule flexible (it doesnt seem to matter if it's 1 or 2 or 10 residues), I keep getting this error in the stderr:

Code: Select all
 Traceback (most recent call last):
  File "/Library/MGLTools/PyRx/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/wxMainFrame.py", line 295, in TryCommand
    retObject = command(*args, **kw)
  File "/Library/MGLTools/PyRx/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/molNavigator.py", line 191, in OpenMolecule
    self.AddMolecule(mol)
  File "/Library/MGLTools/PyRx/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/molNavigator.py", line 241, in AddMolecule
    assembly = self.GenerateAssambly(mol.allAtoms)
  File "/Library/MGLTools/PyRx/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/molNavigator.py", line 327, in GenerateAssambly
    atoms[0].lenAtoms = lenAtoms # hold to this variables since it used in other places
  File "/Library/MGLTools/PyRx/Python.framework/Versions/2.6/lib/python2.6/UserList.py", line 31, in __getitem__
    def __getitem__(self, i): return self.data[i]
IndexError: list index out of range


Any ideas on what's wrong/ how to fix it ?

PyRx is SO much easier to use than the regular ADTools set... if it can just duplicate some core functions then I think it will become my preferred tool by far.
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Re: Flexible ligands Bug ?

Postby sargis » Tue Apr 06, 2010 5:29 pm

Thank you for this message. Could you please attach your pdb file and let me know which residues to select to reproduce this bug? Thank you!
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Re: Flexible ligands Bug ?

Postby alesser » Tue Apr 06, 2010 6:28 pm

Sure.. here's the PDB file... it's just PDB entry 1PTR with the ligand deleted via PyMOL..

It seems like adding any residue causes the error.... but two I just verified individually (each one separately selected) that made the error happen are ASN237 and PHE243

Here's the error I get from the logger... in addition to the std error output I noted above.

ERROR|2010-04-06 11:25:32,853|Error in : <bound method MolNavigator.OpenMolecule of <PyRx.molNavigator.MolNavigator; proxy of <Swig Object of type 'wxPyScrolledWindow *' at 0xf9c600> >>
Attachments
1PTR_ProteinOnly.pdb
PDB entry 1PTR with ligand deleted
(30.97 KiB) Downloaded 294 times
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Re: Flexible ligands Bug ?

Postby sargis » Wed Apr 07, 2010 12:48 am

Thank you for the PDB file. Now I see where the problem is. I'll need to convert PDB into PDBQT before passing it to AD4FlexibleReceptorPreparation. Please use the following workaround for now:
Right-Click (control-click on Mac) on the name of the molecule and select AutoDock -> Make Macromolecule. After this AutoDock -> Flexible Residues should be able to do its job. Thanks!
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Re: Flexible ligands Bug ?

Postby alesser » Wed Apr 07, 2010 4:42 am

So it was nothing specific to that PDB then , but a general program bug ?
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Re: Flexible ligands Bug ?

Postby sargis » Wed Apr 07, 2010 4:21 pm

alesser wrote:So it was nothing specific to that PDB then , but a general program bug ?

Right, it was a general program bug. Thanks!
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Re: Flexible ligands Bug ?

Postby xtaldocstein » Mon May 12, 2014 12:51 pm

I get the same exact error within Pymol using the autodock/vina plugin. How do I fix this same bug in Pymol 1.7.0.0?
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