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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
 
30 Second PyRx Explainer PDF Print
Written by Sarkis Dallakian   

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Last Updated on Tuesday, 10 May 2016 16:19
 
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