Flexible residues output problem

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Flexible residues output problem

Postby GryderArt » Mon Jun 24, 2013 5:29 pm

Dear Sargis,

I am trying to run with flexible residues in PyRx. I made my Macromolecule in PyRx, and then selected Autodock -> Flexible Residues to make the flex and rigid files. I then ran it in the ADVina wizard, and it ran smooth. But then, it is ubable to display the results. The resulting XXX_out.pdbqt is not able to be opened in PyRx or ADTools.

Here is the error message I get when trying to open it:

Code: Select all
Error in : <bound method MolNavigator.OpenMolecule of <PyRx.molNavigator.MolNavigator; proxy of <Swig Object of type 'wxPyScrolledWindow *' at 0x5130a80> >>
Python 2.6.5 (r265:79096, Mar 19 2010, 21:48:26) [MSC v.1500 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> Traceback (most recent call last):
  File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\wxMainFrame.py", line 304, in TryCommand
    retObject = command(*args, **kw)
  File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\molNavigator.py", line 180, in OpenMolecule
    mols = self.ReadMolecule(filename)
  File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\molNavigator.py", line 322, in ReadMolecule
    molecules = parser.parse()
  File "C:\Program Files (x86)\PyRx\lib\site-packages\MolKit\pdbParser.py", line 767, in parse
    self.pdbRecordParser[record](records)
  File "C:\Program Files (x86)\PyRx\lib\site-packages\MolKit\pdbParser.py", line 1809, in parse_PDB_ROOT
    res = self.mol.chains.residues[-ind]
  File "C:\Program Files (x86)\PyRx\lib\UserList.py", line 31, in __getitem__
    def __getitem__(self, i): return self.data[i]
IndexError: list index out of range
>>>



Thanks for helping!
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Re: Flexible residues output problem

Postby sargis » Mon Jun 24, 2013 8:06 pm

Dear Berkley,

Thank you for being active user. Please attach XXX_out.pdbqt so we can reproduce this. Also, how large is your Macromolecule? I had some problems recently with Autodock -> Flexible Residues part. PyRx would crash on 32-bit Windows with no error messages. This is happening with proteins with more than 100 residues in a chain. I traced this down to an inherit limitation of Python recursion depth in http://mgldev.scripps.edu/cgi-bin/viewv ... iew=markup.

Since your Autodock -> Flexible Residues worked fine, you don't have to worry about this. But to troubleshoot XXX_out.pdbqt opening issue, I need to see what your XXX_out.pdbqt looks like, since I haven't seen this error before.

Thank you for using PyRx!
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Re: Flexible residues output problem

Postby GryderArt » Mon Jun 24, 2013 9:58 pm

Sargis,

Thanks! I've attached the output file here. Let me know if you need any other files.
Attachments
AR_Phenyl_c5_HDACi_v2_out.pdbqt
(48.58 KiB) Downloaded 297 times
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Re: Flexible residues output problem

Postby sargis » Mon Jun 24, 2013 11:26 pm

Berkley,

Thanks for the output file. I've used the follwoing steps top open this file, as shown in the image below, and it works fine from me: PyRx -> Vina Wizard -> Analyze Results -> Insert new item (first icon from the toolbar on the left with + sign on it). Please verify that these steps work for you as well. If so, please repeat your steps to see you can reproduce this error. Thanks!
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Untitled.jpg
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Re: Flexible residues output problem

Postby GryderArt » Tue Jun 25, 2013 3:11 pm

Yes, I followed those steps, and got this message:
Code: Select all
Traceback (most recent call last):
  File "C:\Program Files (x86)\PyRx\lib\site-packages\traitsbackendwx-3.3.0-py2.6.egg\enthought\pyface\ui\wx\action\action_item.py", line 476, in _on_tool
    self.controller.perform(action, action_event)
  File "C:\Program Files (x86)\PyRx\lib\site-packages\traitsbackendwx-3.3.0-py2.6.egg\enthought\traits\ui\wx\table_editor.py", line 1598, in perform
    getattr( self.editor, action.action )()
  File "C:\Program Files (x86)\PyRx\lib\site-packages\traitsbackendwx-3.3.0-py2.6.egg\enthought\traits\ui\wx\table_editor.py", line 1186, in on_add
    self.add_row()
  File "C:\Program Files (x86)\PyRx\lib\site-packages\traitsbackendwx-3.3.0-py2.6.egg\enthought\traits\ui\wx\table_editor.py", line 532, in add_row
    object = self.create_new_row()
  File "C:\Program Files (x86)\PyRx\lib\site-packages\traitsbackendwx-3.3.0-py2.6.egg\enthought\traits\ui\wx\table_editor.py", line 510, in create_new_row
    *factory.row_factory_args, **kw  )
  File "C:\Program Files (x86)\PyRx\lib\site-packages\traits-3.3.0-py2.6-win32.egg\enthought\traits\ui\ui.py", line 744, in evaluate
    return function( *args, **kw_args )
  File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\vinaWizard.py", line 824, in my_row_factory
    parent.Open()
  File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\vinaWizard.py", line 796, in Open
    self.AddDocking(filename)
  File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\vinaWizard.py", line 612, in AddDocking
    molecules = parser.parse()               
  File "C:\Program Files (x86)\PyRx\lib\site-packages\MolKit\pdbParser.py", line 767, in parse
    self.pdbRecordParser[record](records)
  File "C:\Program Files (x86)\PyRx\lib\site-packages\MolKit\pdbParser.py", line 1809, in parse_PDB_ROOT
    res = self.mol.chains.residues[-ind]
  File "C:\Program Files (x86)\PyRx\lib\UserList.py", line 31, in __getitem__
    def __getitem__(self, i): return self.data[i]
IndexError: list index out of range
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Re: Flexible residues output problem

Postby GryderArt » Tue Jun 25, 2013 3:13 pm

Are you using 0.8 or 0.9? I'm a windows user with PyRx 0.8
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Re: Flexible residues output problem

Postby sargis » Tue Jun 25, 2013 5:09 pm

GryderArt wrote:Are you using 0.8 or 0.9? I'm a windows user with PyRx 0.8

Good question. I think I used 0.8 version on Windows to produce the screenshot above, but I'm not 100% sure. I'm using my home PC for this.
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Re: Flexible residues output problem

Postby GryderArt » Tue Jun 25, 2013 6:23 pm

Yes, you are using windows 0.8 (I can tell by the way the frame looks). I'm not sure what the problem is.
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Re: Flexible residues output problem

Postby Phonychemist » Fri Apr 11, 2014 2:09 am

Hi GryderArt, I'm having the same issue on two separate boxes with windows 7 using PyRx 0.8 - this only happens when using flexible residues (does not matter how many).

Were you ever able to find a solution to this problem?
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Re: Flexible residues output problem

Postby sargis » Thu Apr 24, 2014 3:10 am

I fixed this in the latest version of PyRx. PyRx 0.9.1 for Windows is currently only $59.99 and it includes many new features and bug fixes - https://sites.fastspring.com/pyrx/instant/pyrx

Please let me know if you have question or need more information.

Thank you for using PyRx!
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