Dear Consortium Members and Affiliates,
Fall has arrived in New England, the air is crisp, the leaves are brightly hued, the academic season is now in full swing, and it's time for the SBGrid October update.
Axel Brunger, one of our first SBGrid members, is featured in this month's SBGrid Tale. Please take a look to learn more about what's happening in this Stanford Professor's laboratory.
Hopefully many of you joined our webinar last week featuring PARTICLE developer, James Chen. If you missed it, please take a look at our Webinar Archive to watch a recorded version of the presentation. Up next is Ronan Keegan's presentation "What's new in CCP4 6.3.0" on Thursday, November 1st.
CCPN reports that the need to develop a long-term plan for sustainability, coupled with a recent loss of funding, have led them to consider charging a small licensing fee. Before finalizing their decision, they are asking for community feedback via the CCPN survey.
Be sure to check out SBGrid's recent publication, "A Quick Guide to Software Licensing for the Scientist-Programmer," in PLoS Computational Biology. Written in collaboration with BerkeleyLaw Samuelson Law, Technology and Public Policy Clinic , this guide is intended to help those of you who write scientific software to navigate the licensing process.
Since our last publication, five new groups have joined SBGrid. Michael Murphy became our second member from University of British Columbia, Yoonsang Cho has joined our growing contingent from Saint Louis University, and from IBS Grenoble we have welcomed the groups of Jerome Boisbouvier, Guy Schoehn, and Juan Fontecilla-Camps.
Welcome to our new members!
We pushed a small software update on October 2 that included Coot 0.7, Gnuplot 4.6.0, O version 14.0.0, PHENIX 1.8.1-1168, RELION 1.1, Sparky 3.115, XDS 20120926, and one new package: the Python Macromolecular Library 1.2.0, which includes TLSView and the mmCIF graphical editor.
Note that the update to Gnuplot may require you to manually specify an older version using a ~/.sbgrid.conf version override file if you are using certain applications, e.g. ATSAS.
Notable Software Changes
COOT was updated to version 0.7, and is notable for introducing RNA modeling tools RCrane and Cootaner, introduction of ligand builder and JLigand interface. For a full list of changes please read the release notes.
Alwyn Jones just released O version 14.0.0 (buteo). All new commands are documented on the A-Z of O section of the website (marked in red).
Phenix was updated to version 1.8.1, which includes a real space refinement protocol for twinned structures, the phenix.merging_statistics utility, and the introduction of Phenix.erraser - an automated RNA model building application developed by the Rhiju Das group at Stanford (see the preprint).
The XDS update (release from Sept 26th, 2012) fixes a bug introduced in the July version.
Python Macromolecular Library 1.2.0 was installed. This application was developed by Ethan Merritt at University of Washington and includes a molecular viewer for TLS rigid body motion.