PyRx – Python Prescription

Virtual Screening Tool

Frequently Asked Questions

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Is there a user’s manual for PyRx?

PyRx is designed to be intuitive to learn, with no manual required. Watching PyRx screencasts is the best way to get started. There is also this excellent video tutorial on ligand docking that is very helpful. Please see the following links for additional information:

How to report a bug.

Please visit http://sourceforge.net/p/pyrx/tickets, click on Log In (if you have SourceForge account) or Join (if you don’t have SourceForge account) and Create Ticket. Please provide information about your Operating System, PyRx version, steps required to reproduce the bug and attach all input files needed. Also, take a screen capture and attach it as well; sometimes it’s simpler to show someone what’s on your screen than it is to explain it.

How do I cite PyRx.

Please refer to the following publication if you’d like to cite PyRx in your article:

Small-Molecule Library Screening by Docking with PyRx. Dallakyan S, Olson AJ. Methods Mol Biol. 2015;1263:243-50. The full-text is available at https://www.researchgate.net/publication/273954875_Small-Molecule_Library_Screening_by_Docking_with_PyRx

How to sort the table in Analyze Results tab.

The user can sort the items in the table based on the values in a column by clicking the header of that column as shown in the image below. Source: TableEditor#managing-items

  • On the first click, the items are sorted in ascending order. The characters >> appear in the column header to indicate that the table is sorted ascending on this column’s values.
  • On the second click, the items are sorted descending order. The characters << appear in the column header to indicate that the table is sorted descending on this column’s values.
  • On the third click, the items are restored to their original order, and the column header is undecorated.

How to reset perspective and restore the default PyRx arrangement?

Use View -> Reset Perspective menu. This is handy in case PyRx crashes and you want to restore the default view.

Keyboard and mouse interaction with 3D Scene.

PyRx is using Mayavi for 3D Scene and all keyboard and mouse interactions are the same as described in Mayavi documentation except for picking interaction. Pressing ‘p’ key on a keyboard shows full name and coordinates of an atom under current mouse position.

How to clean your PyRx workspace.

PyRx uses .PyRx_workspace in your home folder as the default workspace. You can rename/delete that folder and restart PyRx to have a new and clean workspace.

Docking instance has no attribute ‘ligMol’.

This error message shows up when there are no docked conformation in the docking log file. To troubleshoot this problem please open your dlg file and read it carefully to see why there were no docked conformation recorded there.

Too many torsions.

AutoDock sets the maximum number of torsions a ligand can have. When a ligand has more than this maximum number of torsions, you’ll get “FATAL ERROR: PDBQT ERROR: too many torsions, maximum number of torsions is 32” error message. To run AutoDock with ligands that have too many torsions, limit the number of active torsions before making pdbqt files using Edit > Preferences > AutoDock > Ligand Preparation > Number of torsion: option. Set this to, say, 32 and remake ligand pdbqt file(s).

How to run PyRx on a cluster.

PyRx enables Cluster execution mode when, in addition to AutoDock binaries, you also have qsub (PBS or SGE) in your path. Please install PyRx on the head node and make sure that AutoDock binaries are available from all the nodes. PyRx creates individual job files for each protein-ligand docking and submit all the jobs to your cluster.

Location of PyRx source code in the binary distribution.

After installing PyRx using binary distribution you can find PyRx source code at:

  • Windows – C:\Program Files (x86)\PyRx\$Version\Lib\site-packages\PyRx
  • Linux – /usr/local/PyRx-$Version/lib/python2.6/site-packages/PyRx
  • Mac –  /Library/PyRx/$Version/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx

where $Version is version number for PyRx binary distribution.

Where PyRx stores the data.

By default PyRx stores data in the following folders depending on the OS:

  • Windows – C:\Users\$UserName\.PyRx_workspace (Windows Vista and higher)
  • Linux – /home/$UserName/.PyRx_workspace
  • Mac – /Users/$UserName/.PyRx_workspace

where $UserName is your user name. This can be changed using Edit > Preferences > Workspace option. You can also find the path of different entities under Navigator > AutoDock by right-clicking on an item and select Properties option.

How to remove/uninstall update.

If you experience problems after updating PyRx using Help > Check for Updates… menu, please remove the following folder to disable this update:

  • Windows – C:\Users\$UserName\.PyRx_workspace\update (Windows Vista and higher)
  • Linux – /home/$UserName/.PyRx_workspace/update
  • Mac –  /Users/$UserName/.PyRx_workspace/update

where $UserName is your user name.

How many jobs can I run at once?

This depends if you are using AutoDock 4 or Vina, and the execution mode you select for the corresponding wizards.

  • If Local execution mode is selected when you start AutoDock Wizard, then PyRx would use the number of available CPUs to decide how many docking jobs to run at once. By default, this number is set to the number of CPU cores minus one (or one, if there is only one CPU core available). For instance, if you have a PC with 8 CPU cores, PyRx runs 7 docking jobs at once. This number can be changed using PyRx > Edit > Preferences… menu. For Vina jobs, PyRx submits one job at a time, since Vina can utilize all available CPUs.
  • On a Linux cluster, there is additional execution mode available called Cluster. If you select that, PyRx would submit all the jobs at once to your cluster.

How to select all the ligands for virtual screening at once.

Click on the first ligand, scroll down and Shift click on the last ligand. This will select all the ligands for virtual screening at once.