We are pleased to announce the release of PyRx 0.9.2. One of the main new feature implemented in PyRx 0.9.2 is an option to execute AutoDock 4 or Vina using remote execution mode as shown in the image below. This is a great feature for users who want to run docking on a remote cluster…

To make protein side chains flexible during the docking, please load the molecule in PyRx using File > Load Molecule and click on + sign next to the molecule in Navigator > Molecules panel to see the list of residues. Then using Shift or Control keys, select residues you wish to make flexible. You can click…

We are pleased to announce the release of PyRx 0.9.1. This is a minor bugfix release. PyRx 0.9 users, please use PyRx > Help > Check for Updates…  menu to update. The following is a new feature and a bug fix implemented for 0.9.1 release: [r151] Added stereo rendering option to 3D scene. Click on…

We are pleased to announce the release of PyRx 0.9. The following are new features and bug fixes implemented for 0.9 release: [105] Vina Wizard is now using the number of CPUs (–cpu option). Please use Edit > Preferences and enter Available CPUs to specify this number. By default, PyRx sets it to the number…

I wrote this small script that can be used to rotate molecules in PyRx. You can try it by downloading rotate.py and then use File → Run Python Script menu from PyRx to run it. To stop this rotation, click on Python Shell tab under Controls panel, type stop() and hit Enter. The following is…

This post explains how to install NVIDIA proprietary drivers on CentOS 6. By default, CentOS 6 comes with nouveau drivers, which for 3D (OpenGL) rendering, is order of magnitude slower that NVIDIA’s proprietary drivers.  For instance, I had glxgear running at round 400 frames per second (FPS) before installing NVIDIA proprietary drivers and at around…

I was looking for a sample code and found Nullege search engine for Python source code to be very useful. There are other search engines that do similar work, such as Google Code Search and Koders.com, however, Nullege seems to be the best one for Python. I have found the following excellent projects that I…

I’m pleased to announce the release of PyRx 0.8. Here is what’s new in this new release: Version 0.8 – 30 December 2010 [84] Implemented Vina Web Services client and added remote executaition mode for Vina wizard. [83] Changed web service URI from http://ws.nbcr.net to http://kryptonite.nbcr.net. Opal client distributed with PyRx is compatible with Opal2…

I was looking for an open source project that would do small molecule alignment and I finally found it. There are many publications out there that describe different algorithms for small molecule alignment, but I couldn’t find any that I can try myself. I was very excited to read release announcement for Piramid that does exactly what…