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Recent Changes in Vina Web Services and Mac OS X Updates PDF Print
Written by Sarkis Dallakian   

There has been recent changes in Vina web services that makes it impossible to run Vina in Remote (Opal Web Services) mode. I've uploaded new updates to fix this.  Please use PyRx > Help > Check for Updates... menu to apply this update if you are using Linux or PyRx 0.9.7 or higher on Windows. Unfortunately PyRx update procedure doesn't work on Mac OS X or on Windows with PyRx 0.9.6 and earlier versions. Please use the following steps to update PyRx instead.

Step 1, visit https://sourceforge.net/p/pyrx/code/HEAD/tree/ and click on Download Snapshot.

Step 2, uncompress this downloaded file and locate PyRxDev/PyRx folder.

Step 3, make a backup copy of the following folder, by renaming it to PyRx.bak for instance, in case PyRx fails to start after this update:

  • Windows PyRx 0.9.6 or older - C:\Program Files (x86)\PyRx\0.9.6\Lib\site-packages\PyRx
  • Mac OS X - /Library/PyRx/$Version/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx

$Version here is the version number of PyRx (e.g. 0.9.6)

Step 4, replace this folder with the one you downloaded above.

If you have updated PyRx previously using Help > Check for Updates... menu, delete .PyRx_workspace\update from your home directory.

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

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Last Updated on Saturday, 07 April 2018 14:02
 
FLOSS Weekly 464: PyRx PDF Print
Written by Sarkis Dallakian   
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PyRx 0.9.7 Release Announcement PDF Print
Written by Sarkis Dallakian   

We are pleased to announce the release of PyRx 0.9.7. We have upgraded Python interpreter on Windows to 64 bit version that allows users to work with larger molecules. Other major changes in this release include:

For Inverse Virtual Screening with Vina, we now have preferences page where users can specify maximum number of Macromolecules to load.

097_inverse_preferences.png

Added Lipinski Rule of Fives in Open Babel table filter.

097_lipinski.png

Open Bable table now includes logP, number of hydrogen bond donors (#HBD) and acceptors (#HBA) columns.

097_openbable_table.png

Implemented Max Runtime in PyRx > Edit > Preferences. Users can change this to terminate all local jobs that take more than Max Runtime (in minutes) to run.

097_max_runtime.png

PyRx 0.9.6 users can update to this release using PyRx > Help > Check for Updates... menu. The list of changes for 0.9.6 version is available at PyRx 0.9.6 Release Announcement.

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Last Updated on Saturday, 14 October 2017 06:39
 
PyRx 0.9.6 Release Announcement PDF Print
Written by Sarkis Dallakian   

We are pleased to announce the release of PyRx 0.9.6. Major changes in this release include:

When making pdbqt for Macromolecules that have atoms at alternate locations, users can now generate all possible combinations.

096_generateall.png

Individual residues can now be displayed as Balls and Sticks.

displayresidueballsandsticks.png

A new option to choose Formula_Title for the name of the ligands when making AutoDock Ligand pdqt files using Open Babel widget. Use PyRx > Edit > Preferences, click on + icon next to Open Babel and select AutoDock Ligand. You'll see a new option there next to "Name Converted Ligand Using". There are two options: Title or Formula_Title. If you select Formula_Title, next time when PyRx makes AutoDock ligands using Open Bable, it will name ligands accordingly.

096_op_ligand_name.png

Option to toggle on and off balloon widget shown below.

096_toggle_balloon.png

PyRx 0.9.5 users can update to this release using PyRx > Help > Check for Updates... menu. The list of changes for 0.9.5 version is available at PyRx 0.9.5 Release Announcement.

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PyRx 0.9.5 Release Announcement PDF Print
Written by Sarkis Dallakian   

 We are pleased to announce the release of PyRx 0.9.5. Major changes in this release include:

  • Fixed a bug when toggling hydrogen bonds using toolbar icon.
  • PyRx can now run docking for molecules that have quotes in their names, like in 3-hydroxy-5_7_3'_4'_5'-pentamethoxyflavone.
  • Added balloon widget to draw labels when the mouse stays above a molecule. This can be helpful when there are multiple molecules in 3D scene. The mouse cursors changes to busy when you move the mouse over a molecule. You can disable this by deleting a single line - https://sourceforge.net/p/pyrx/code/278/tree/PyRxDev/PyRx/mayaviEngine.py#l110 . Let me know if you don't like this feature; I can add an option to disable this in the next release of PyRx, if needed.

pyrx-balloon

  • Added RMSD from reference structure column to AutoDock Analyze Results table.

pyrx-rmsd

  • When making flexible residues, PyRx is now using options defined in receptor preparation preferences to decide what type of changes to do.

pyrx-preferences

PyRx 0.9.2, 0.9.3 and 0.9.4 users can update to this release using PyRx > Help > Check for Updates... menu. The list of changes for 0.9.4 version is available at PyRx 0.9.4 Release Announcement.

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Last Updated on Sunday, 22 January 2017 17:18
 
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