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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
 
PyRx Ligand Docking Tutorial PDF Print
Written by Sarkis Dallakian   

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Last Updated on Saturday, 10 December 2016 19:46
 
2016 Year in Review PDF Print
Written by Sarkis Dallakian   

2016 has been a great year for PyRx. We have passed 35k downloads, which is excellent for a scientific software. There have been many new publications mentioning PyRx; it's nice seeing PyRx used for research ranging from Anticancer to Zika. PyRx now has a Facebook page and we also run Facebook and Googe AdWords advertising. The best news for 2016 is that we moved to our new headquarters with a beautiful view of Bonita Golf course shown in the photo below. Have a great holiday season!

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Last Updated on Tuesday, 06 December 2016 04:29
 
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