What up, players?! SBGrid newsletter in da house! Aww yeah!
Our latest structural biology tale features a member of the Consortium from Australia. Marc Kvansakul joined the consortium in October 2010 and is a former trainee of Peter Colman. Now in his own lab at La Trobe University, Marc is working with a medicinal chemist to identify small molecules that block BHRF1's anti-apoptotic function. Please read more about Marc on the SBGrid website.
We also want to highlight several publications by SBGrid members in the last month, including the structure of cryptochrome from Brian Crane's lab at Cornell, the structure of the HIV-1 gp120 V1/V2 domain with PG9 antibody from Peter Kwong's lab at NIH and the structure of Lin28/let-7 microRNA complex from Piotr Sliz' Lab here at Harvard. A list of all recent publications from SBGrid member laboratories is available on our website.
Please join us Monday, January 9th at 4:00pm for an Afternoon Tea with Wladek Minor. This 30-minute webinar on HKL2000 will be presented by Wladek Minor, Professor of Molecular Physiology and Biological Physics at University of Virginia Health System. For more details visit the SBGrid website.
Please note that Harvard University shuts down most operations during the week between Christmas and New Years. We'll be checking email occasionally, but most regular work with be delayed until the new year.
We have a small update planned for later today that includes new versions of PHENIX, EMAN2, ModelFree, PyMOL and Graphviz as well as two new programs: ANODE and Rmerge.
Yo Happy Holidays!
The following software updates will be available later tonight or tomorrow:
Linux and Mac OS X Intel
PHENIX has been updated to version 1.7.3-928. The PHENIX website has a wealth of information including a change log and the [updated PHENIX manual][phman]. Requested by everyone.
EMAN2 has been updated to version 2.04. The release annoucement has details of the new features and fixed bugs and the EMAN2 wiki has tutorials, documentation and more. Requested by Wolf Lab, OIST.
ModelFree has been updated to version 4.20. This is mostly a bug fix update. There is a short change log on the ModelFree home page as well as the ModelFree manual.
ANODE is the latest addition to the SHELX package developed by George Sheldrick and is used for ANOmalous electron DEnsity analysis. This application is still in beta-testing, and it's available to labs that have a SHELX license in the beta-20111128 directory. The open access paper describing the software is available from the Journal of Applied Crystallography. Requested by IBS Grenoble.
Rmerge is a new package that can calculate Rpim for merging. There is no manual, but a basic description of its capabilities and use can be found in Cell 147, pp 199-208. Requested by the Mayer Lab at NIH.
Graphviz has been updated to version 2.28.0. Requested by the Springer Lab at the Immune Disease Institute.
PyMOL version 1.5.0b3 has been added to the software tree. This is the latest beta for the upcoming PyMOL 1.5.0. The Mac version has also been added to the software tree, but it crashes when run from an NFS server. We have a filed a bug report with Schrodinger over the issue.
We biffed the shell configuration files for our transition to the 64-bit software branch on 32-bit Ubuntu and Debian hosts. We tweaked the shell configuration and those linux distributions are now using the correct software branches. Reported by Robert Campbell, Queens University and Andrew Ring, UC Berkeley.
Various ModelFree binaries were crashing on Fedora 14. We updated the ModelFree installation to run on newer linux distributions. Reported by Adrien Favier at IBS Grenoble.
SPIDER was missing its traditional symlink after the last update. Instead of relying on a dumb symlink, we added a script that will dynamically pick the most suitable SPIDER binary for your platform. Suggested by Sabuj Pattanyek, Vanderbilt University.
O, Coot and a few other OpenGL-based applications were inadvertently broken with the introduction of a rogue libGL.so.1 library on linux. We removed the library, and things returned to normal. Reported by lots of people. Doh!
CCPNMR crashed due to a library error on some OS X Intel hosts. We rebuilt CCPNMR to resolve the problem. Reported by Remy Sounier, Chou Lab at HMS.
SPIDER on 64-bit linux platforms was using an absolute symlink to point to the i386-linux/spider directory. This caused the update scripts to generate shell configurations without any SPIDER settings at some sites. We fixed this by making the symlink relative and forcing the remote sites to update. Reported by lots of people.
ROSETTA on OS X Intel was missing some of its dependent libraries. The application was relinked to point to the correct libraries. Reported by Juan Mendoza, Garcia Lab, Stanford.
Thanks for your bug reports!