Problem with selecting flexible residues

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Problem with selecting flexible residues

Postby pankajM » Tue Jul 08, 2014 10:13 am

Dear Sargis,

I am using PyRX 0.8, when I chose flexible residue by selecting individual amino acid, it takes some time saying 'creating flexible residues' but return with the following error:

Traceback (most recent call last):
File "D:\Program Files\PyRx\lib\site-packages\PyRx\molNavigator.py", line 164, in OnFlexResidues
if self.frame.vsModel.flex_residues:
AttributeError: VSModel instance has no attribute 'flex_residues'

Please help!
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Re: Problem with selecting flexible residues

Postby sargis » Wed Jul 09, 2014 1:17 am

Dear pankajM,

Please try upgrading to PyRx 0.9 which is currently only $59.99. This has probably been fixed in PyRx 0.9 and I'll be happy to fix any bugs you might encounter with the latest version of PyRx.

Thank you for using PyRx.
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Re: Problem with selecting flexible residues

Postby pankajM » Tue Jul 15, 2014 5:50 am

Dear Dr. Sarkis

I purchased PyRx 0.9.2 and installed it on window with already installed python 3.4.1. Again, when I chose flexible residues the program show a error message 'pythonw.exe has stopped working' and then it crashed.

Please help!
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Re: Problem with selecting flexible residues

Postby sargis » Tue Jul 15, 2014 12:32 pm

Thank you for purchasing PyRx 0.9.2 and sorry about that. Making side chains flexible currently works only for small proteins with fewer than 200 residues. I'll try to find a fix for this and provide updates. I'm thinking that the workaround might be to cut the protein into smaller parts, do pdbqt conversion with flexible residues and then past the result into final pdbqt for the whole protein. If you can send me the pdb file or upload it as an attachment here and let me know which residues to make flexible, I'll be happy to use it as a first test case.

Thank you!
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Re: Problem with selecting flexible residues

Postby pankajM » Tue Jul 15, 2014 1:31 pm

Dear Dr. Sargis
Thank you very much for your reply and am glad for your ready efforts. Attached is the pdb file and the flex_residues are: PHE1145, GLU1266, ASN1578, GLU1168, VAL1580, CYS1191.
E-MAIL: pankaj.mishra.phe11@iitbhu.ac.in
Attachments
rec_pankajM.rar
Receptor_flex_res
(147.13 KiB) Downloaded 97 times
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Re: Problem with selecting flexible residues

Postby pankajM » Wed Jul 16, 2014 6:30 am

Dear Sargis

Sorry for troubling you again! I encountered with one more issue here, while analysis of docking run I need to save the pose but not necessarily the highest ranked. As suggested in other post to save it through sdf whenever I save the other pose (not the top one), it goes to the top one only.

Thank you

Pankaj
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Re: Problem with selecting flexible residues

Postby sargis » Sat Jul 26, 2014 11:55 pm

Dear Pankaj,

Sorry for the late reply. You can save a specific pose by selecting that pose and right-clicking on it under Molecules tab and selecting Save as PDB as shown in the attached image.
Untitled.png
Untitled.png (10.55 KiB) Viewed 4020 times


There is also an option under Edit -> Preferences.. called "Number of Poses to Retain" as shown in the second attached image. This can be used to save top n poses.
pyrx_pref.png
pyrx_pref.png (46.54 KiB) Viewed 4020 times

If you have set this to 1, that would explain why only top pose is saved in sdf.

Please let me know if this helps with the problem of saving poses.

Thank you,
Sargis
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Re: Problem with selecting flexible residues

Postby sargis » Mon Aug 11, 2014 5:02 am

pankajM wrote:Thank you very much for your reply and am glad for your ready efforts. Attached is the pdb file and the flex_residues are: PHE1145, GLU1266, ASN1578, GLU1168, VAL1580, CYS1191.

Created new update for making flexible residue to work for larger proteins. Please use PyRx > Help > Check for Updates... menu and let me know if that fixes this.

I have a test case with this pdb and flex_residues running that includes rec_pankajm_flex.pdbqt and rec_pankajm_rigid.pdbqt files temporarily stored at:
http://nbcr-222.ucsd.edu/opal-jobs/appv ... 426062923/

Thank you for using PyRx!
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Re: Problem with selecting flexible residues

Postby pankajM » Mon Aug 11, 2014 7:53 am

Dear Sargis,

It's working fine. Thank you very much!

best

Pankaj
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Re: Problem with selecting flexible residues

Postby sargis » Tue Aug 12, 2014 12:56 am

Dear Pankaj,

You are welcome. I have found another bug that causes problems parsing output files when flexible residue number is greater than 999. To fix this please edit C:\Program Files (x86)\PyRx\0.9.2\Lib\site-packages\AutoDockTools\MoleculePreparation.py, search and replace BEGIN_RES %s %s %4s with BEGIN_RES %s %s %s (2 places). Then recreate flex.pdbqt and rerun the docking.

Best,
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