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.
How to clean your PyRx workspace?
PyRx uses .mgloots/PyRx in your home folder as the default workspace. You can rename/delete that folder and restart PyRx to have a new and clean workspace. See also: How can I get rid of old ligands?
Is there a user's manual for PyRx?
Not yet. PyRx is designed to be intuitive to learn, with no manual required. Watching PyRx screencasts is the recommended way to get started. Imaging how many people would use a web browser if reading a manual was required. In fact, PyRx is using Advanced User Interface Library, which was developed by Kirix Corporation and used in their data browser.
What's causing "Open dlg file for details" error message?
When there are no docked conformation in the docking log file, PyRx shows the following error message.
Open output.dlg for details.
Docking instance has no attribute 'ligMol'
Docking instance has no attribute 'ligMol - is the error message that dlg parser throws. "Open "+outputFile+" for details" - is the message PyRx prints when it catches this exception. To troubleshoot this problem you need to open your dlg file and read it carefully to see why there were no docked conformation recorded there.
How to run PyRx on a server?
This depends on the server and wether you are planning to run AutoDock 4 or Vina. For AutoDock 4:
- If it's a standalone server, then you can install AutoDock and PyRx on that server and set AutoDock path using Edit -> Preferences menu. PyRx enables Local execution mode when it finds AutoDock binaries in your path.
- If it's a cluster where you can submit batch script using qsub (PBS or SGE), then you can install PyRx on the head node and make sure that AutoDock binaries are available from all the nodes. PyRx enables Cluster execution mode when, in addition to AutoDock binaries, you also have qsub in your path.
- If you want to submit jobs remotely, then you'll need to install Opal Toolkit on the server and deploy AutoDock services so that PyRx can communicate with the server and submit AutoDock jobs. You can then specify the URI of the server and which services to use using Edit -> Preferences -> AutoDock -> Web Services. Please refer to Opal Documentation for instructions on how to install Opal Toolkit. Note that, by default, PyRx is using http://ws.nbcr.net cluster and Remote execution mode is always enabled.
Instructions for Vina are similar except that there is no remote execution mode. As of this writing (10/27/2010), Vina is not yet in the list of applications that are available on NBCR server.
Do I need an account to use NBCR web services?
No account is need to access NBCR web services. You can submit jobs using PyRx or through online submission forms. Please cite Opal Toolkit in your publication when you use Remote (Opal Web Services) mode.
How do I cite PyRx?
Please refer to the following publication if you'd like to cite PyRx in your article:
How can I join PyRx project?
Please visit PyRx Developer Trac for information on how to join PyRx project. Thanks!