The problem with installation PyRx.

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The problem with installation PyRx.

Postby Michael Gol » Thu Sep 19, 2013 11:09 am

Hi,

I have a problem with running the PyRx in every version available on the official website. I have windows 7
The installation is aborted.

The problem looks like this:


error deleting "C:/Program Files/PyRx/Lib/site-packages/vtk": directory not empty
error deleting "C:/Program Files/PyRx/Lib/site-packages/vtk": directory not empty
while executing
"file delete $force $dir"
(procedure "::InstallJammer::UninstallDirectory" line 2)
invoked from within
"::InstallJammer::UninstallDirectory {C:/Program Files/PyRx/Lib/site-packages/vtk}"
("eval" body line 1)
invoked from within
"eval ::InstallJammer::UninstallDirectory $dir"
(procedure "::InstallJammer::CleanupCancelledInstall" line 53)
invoked from within
"::InstallJammer::CleanupCancelledInstall"
(procedure "::InstallJammer::exit" line 42)
invoked from within
"::InstallJammer::exit"
(procedure "::InstallJammer::FinishEventHandler" line 7)
invoked from within
"::InstallJammer::FinishEventHandler .wizard"
(command bound to event)



Can anyone knows how can I solve it?

I also have a few questions about molecular docking, I have to write a paper engineering that involves a comparison of the three programs Autodock 4, Autodock Vina and Dock 6
Plan my work, then download the database PDBbind-CN protein complexes in the format (.pdb) and then convert it to AutoDock format (.pdbqt) in the OpenBabel, then I need to calculate the scorring function in these programs, and then compare the data contained in the database PDBbind-CN (PKD value). Is this a good solution?

Can anyone have an idea how to do it in the simplest possible way? With what program / ​​inteface? PyRx? ADT? Can it be done directly from the cmd on windows?
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Michael Gol
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Re: The problem with installation PyRx.

Postby sargis » Sun Sep 22, 2013 7:26 pm

Michael Gol wrote:I have a problem with running the PyRx in every version available on the official website. I have windows 7
The installation is aborted.

The problem looks like this:

error deleting "C:/Program Files/PyRx/Lib/site-packages/vtk": directory not empty
error deleting "C:/Program Files/PyRx/Lib/site-packages/vtk": directory not empty
while executing
"file delete $force $dir"
(procedure "::InstallJammer::UninstallDirectory" line 2)
invoked from within
"::InstallJammer::UninstallDirectory {C:/Program Files/PyRx/Lib/site-packages/vtk}"
("eval" body line 1)
invoked from within
"eval ::InstallJammer::UninstallDirectory $dir"
(procedure "::InstallJammer::CleanupCancelledInstall" line 53)
invoked from within
"::InstallJammer::CleanupCancelledInstall"
(procedure "::InstallJammer::exit" line 42)
invoked from within
"::InstallJammer::exit"
(procedure "::InstallJammer::FinishEventHandler" line 7)
invoked from within
"::InstallJammer::FinishEventHandler .wizard"
(command bound to event)
Can anyone knows how can I solve it?

Thanks for the message. Please make sure PyRx download is complete and then delete C:/Program Files/PyRx/ folder before installing a new version. This shouldn't be a problem with the latest 0.9 version of PyRx for Windows.

Michael Gol wrote:I also have a few questions about molecular docking, I have to write a paper engineering that involves a comparison of the three programs Autodock 4, Autodock Vina and Dock 6
Plan my work, then download the database PDBbind-CN protein complexes in the format (.pdb) and then convert it to AutoDock format (.pdbqt) in the OpenBabel, then I need to calculate the scorring function in these programs, and then compare the data contained in the database PDBbind-CN (PKD value). Is this a good solution?

Can anyone have an idea how to do it in the simplest possible way? With what program / ​​inteface? PyRx? ADT? Can it be done directly from the cmd on windows?

You can do most of this in PyRx except running Dock 6, since PyRx doesn't have interface for Dock 6. You can, however, run Autodock 4 and Autodock Vina with PyRx and output docking results as SDF or CSV file. You can then run Dock 6 with DOCK Blaster or Chimera and write scripts to compare Autodock 4, Autodock Vina and Dock 6 results. All of this can be done directly from the cmd on windows, except viewing 3D structures.
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