Last chance to apply to attend Open Babel users' workshop

Apply before Apr 22nd to attend the 2nd Open Babble, a hands-on Open Babel workshop presented by Open Babel developers Chris Morley, Tim Vandermeersch and Noel O'Boyle. This will take place on July 5-6 2011 at the Unilever Centre in the Dept of Chemistry, University of Cambridge, UK.

This is the first ever users' workshop for Open Babel, one of the most widely used cheminformatics toolkits. Open Babble presents a unique opportunity to learn how to make the most of Open Babel, whether you are interested in using for converting file formats, writing scripts to analyse molecular structures, or developing your own chemistry software.

The workshop will start on the afternoon of the 5th July, and finish on the evening of the 6th. The exact topics covered will depend on the attendees’ interests but will include some or all of the following:

• Exploiting the Open Babel command line for fast searching and filtering of molecular databases
• How to get the most from the Open Babel GUI
• Getting started with Python scripting for chemistry
• Compiling C++ programs that use Open Babel
• Writing a new plugin for Open Babel
• How to create a user-defined molecular fingerprint
• Combining Open Babel with other Open Source cheminformatics toolkits

To apply, see the workshop website.

Review of Data Analysis with Open Source Tools

A little while ago, I reviewed Gnuplot in Action by Philipp Janert. One of the aspects of that book that I liked the most was the inclusion of more general discussions about data analysis and appropriate methods.

Now Philipp has published a book where those discussions are the focus, and the software is mentioned in passing. Data Analysis with Open Source Tools was published in January 2011 by O'Reilly.

I got my hands on a review copy and gave it a write-up in Journal of Cheminformatics:

...This is a real practitioner's book. Janert, a former physicist and software engineer, is a consultant in data analysis and mathematical modelling. He has taken his hard-won knowledge and tried to get it all down on paper for the reader's benefit. For example, in a chapter with the provocative title of "What you really need to know about classical statistics" he explains why introductory statistics textbooks seem to cover methods and topics at odds with the problems data analysts deal with day-to-day; essentially classical methods were developed at a time of small and expensive datasets and no computational power, and hypothesis testing focused on determining whether an effect existed. Today we have ample computing power and may be dealing with very large datasets; also, we are usually more interested in the size of an effect (practical significance) rather than just whether it exists (statistical significance)...

To read the full review, head on over to J. Cheminf. 2011, 3:10.

Playing GAMESS with Avogadro and wxMacMolPlt

I've put together a tutorial to show how to setup, run and analyse basic QM calculations using Avogadro, GAMESS and wxMacMolPlt (respectively). It is aimed at complete beginners to QM calculations (although with a basic knowledge of the theory).

You can check it out here.

The topics covered are:

• Install required software
• Looking at GAMESS output
• Molecular orbitals of water
• Vibrational frequencies of water
• Effect of basis set
• Conformations of a cyclohexane

Contributions to additional tutorials or suggestions for improvement are most welcome.

PyRx - AutoDocking made simple

I recently presented an AutoDock tutorial at the EBI based around PyRx 0.8, an impressive GUI for AutoDock and Vina by Sargis Dallakyan. It worked out very well, and a big thanks to James Watson from the EBI who helped install all the software. While PyRx still has a few rough edges, it is an order of magnitude easier to use than the existing AutoDock GUI AutoDockTools (although the latter allows more fine-grained control).

We followed the 2010 PyRx tutorial (PyRx2010_rvsnALP_7122010.pdf) available from http://pyrx.scripps.edu/SI/2010/. You will also need the 3D.sdf from that location. You may also want to download sample.tar.gz.

The following notes describe how to get everything set up on Windows:
(1) Download AutoDock 4.2. When installing, install to "C:\Program Files (x86)\AutoDock" not C:\Windows\system32 as suggested.
(2) Download and install PyRx 0.8. This installs to "C:\Program Files (x86)\PyRx".
(3) Replace the appropriate file in "C:\Program Files (x86)\PyRx\Lib\site-packages\PyRx" with importWizard.py, dbPlot.py and autodockNavigator.py.
(4) Have everyone start PyRx (there should be a shortcut on the desktop, else run PyRx.bat) and under Edit/Preferences set the location of AutoDock to "C:\Program Files (x86)\AutoDock\autodock.exe" (they can just browse to the folder and file), and similarly for AutoGrid. If they did this properly, the "Local" radiobutton in the bottom of the AutoDock Wizard tab should be available. They should choose this during the docking.

It should then be possible to work through the tutorial without problems. The tutorial involves docking a single molecule with AutoDock, then running a virtual screen with Vina (I recommend only choosing 5 molecules unless you have lots of time on your hands).

Note that pdbqt files, configuration files and such are saved into C:\Users\MyName\.mgltools\PyRx, if you want to have a look. You can delete this folder to reset PyRx. And all of this software should work equally well on Mac and Linux, although I haven't tested this.

Announcing 2nd Open Babble - Pre-registration now open

Pre-registration is now open for the 2nd Open Babble, a hands-on Open Babel workshop presented by Open Babel developers. This will take place on July 5-6 2011 at the Unilever Centre in the Dept of Chemistry, University of Cambridge, UK.

The workshop will start on the afternoon of the 5th July, and finish on the evening of the 6th. The precise topics to be covered will depend on the attendees’ interests but we anticipate covering topics such as how to get the most from the Open Babel command line applications and the GUI, to writing Python scripts and developing software based on the Open Babel library.

Since only 20 places are available, we are running a pre-registration process to select a diverse range of attendees, from novices to expert users, and from both academia and industry. The registration fee will be €70 for academics, and €220 for industry attendees. This includes one lunch and dinner, but does not include accommodation.

We also note that sponsorship opportunities are available.

To register your interest in attending, please email openbabble@gmail.com before April 22nd with the following information:

Name: _______________
Position: ______________ (e.g. PhD student)
Address: ___________________
Email: _________________
Registration fee: €70/€220
Reason that you should be selected to attend (max three sentences):
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
Topics you would like covered: ____________________________________________
___________________________________________________________________________
___________________________________________________________________________


Regards,
Noel O'Boyle
(On behalf of the Open Babble organisers)

Confab, a systematic conformation generator, published in J Cheminf

My paper on Confab has just been published by the Journal of Cheminformatics. Confab is a systematic (and exhaustive) conformation generator that uses a torsion-driving approach to generate all diverse (by RMSD) low-energy conformers.

Confab - Systematic generation of diverse low-energy conformers NM O'Boyle, T Vandermeersch, CJ Flynn, AR Maguire, GR Hutchison. Journal of Cheminformatics 2011, 3:8.

The software itself is available from http://confab.googlecode.com.

Here's the abstract of the paper:

Background
Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-energy conformers according to a diversity criterion.

Results
Confab generates conformations using the 'torsion driving approach' which involves iterating systematically through a set of allowed torsion angles for each rotatable bond. Energy is assessed using the MMFF94 forcefield. Diversity is measured using the heavy-atom root-mean-square deviation (RMSD) relative to conformers already stored. We investigated the recovery of crystal structures for a dataset of 1000 ligands from the Protein Data Bank with fewer than 1 million conformations. Confab can recover 97% of the molecules to within 1.5 A at a diversity level of 1.5 A and an energy cutoff of 50 kcal/mol.

Conclusions
Confab is available from http://confab.googlecode.com.

Can we use game consoles for chemistry? Yes WiiChem

I've written about using the Kinect to control Jmol, but there's another game console gadget that's been around for some time that offers similar possibilites - the Wii Remote or more simply, the "Wiimote".

A few days ago, Eric Henon and Mickaël Gadroy of the University of Reims announced the WiiChem project on the avogadro-discuss mailing list:

We are pleased to announce that it is now possible to carry out the Wiimote possibilities into Avogadro.

The Wiimote gives the opportunity to use a cheap, easy and flexible device for educational purposes for example. By pointing a Wiimote at a screen you can create, rotate, substitute atom by fragment, ... molecules. Also, you can use it with projector.

Anaglyph (Red-Cyan)/3D possibilities have been implemented.

The feeback (rumble functionality) can be used to check « on the fly » proximities between the molecular system and the manipulated atom.

This is still a Beta version. The src plugin as well as all instructions to compile it are available at :
https://github.com/mickaelgadroy/wmavo

It would be nice to finally see one of the open source 3D viewers come with this functionality out of the box, so this is a very exciting development.

For more information or if you want to get involved, see the Avogadro mailing list, the github repo, or the website for the project (English/French).

Image credit: maury.mccown