Newsletter Jun 2011

Newsletter for June, 2011

Dear Consortium Members and Affiliates,

Ah, Summer has finally arrived (in the Northern hemisphere; apologies to our Australian members). The students have all gone, and Boston traffic has receded from intolerable to merely uncomfortable. I'm looking forward to a quiet summer of frisbee on the Quad and compiling FORTRAN applications. Life's simple pleasures.

We are happy to announce a special one day symposium for members of the SBGrid community. The event will take place on Friday, June 24th at Harvard Medical School, and software developers of some major structural biology tools will present. Space in the event is almost sold out, but we will be offering a WebEx option for non-local members and overflow attendees. The fee to register for all lectures is $120 for on-site attendance or $45 for WebEx attendance. To view the full agenda and register, please visit the SBGrid Developer Symposium registration page.

The word on the street is that OS X 10.7 will be shipping in early July. We should have a copy for internal testing shortly, and we expect it to be a fully supported release as soon as it's available. If you happen to have a pre-release copy and encounter any software bugs, please open a ticket.

We have a quick update planned for today that includes updates for xia2, adxv, T-Coffee, VMD, AUTO3DEM, the PHENIX nightly release, the R statistical computing package and two new packages: CMView and breseq. We also have a beta release of CCP4 6.2.0 in the tree, but there are some caveats you should know before using it.

Happy Summer!

New Members

We've had a busy last month with 7 new members joining the SBGrid Consortium, including two from new institutions.

James Bradner at Dana Farber Cancer Institute in Boston.

Debbie Kelly, an alumnus from an SBGrid member lab, now has her own lab at Virginia Tech Carilion.

Mike Lewis at the St. Louis School of Medicine.

Navej Toor at the University of California, San Diego.

Dong Wang at the University of California, San Diego.

Calvin Yip joins us from the University of British Columbia. UBC is a new institution for SBGrid.

Ning Zheng joins current member Tamir Gonen as our second member from the University of Washington.

Welcome to all of our new members!

Software Updates

The following software updates will be available later tonight or tomorrow:

Linux and Mac OS X (Intel and PPC)

xia2 has been updated to version This version contains some important bug fixes, but not many new features. Graeme Winter, the developer, maintains a xia2 blog for news and updates. Requested by Schiffer Lab at Umass Medical School and the beamlines and a few others.

axdv has been updated to version 1.9.8. This is also a bug fix release. Usage notes area available on the developer's website.

Linux and Mac OS X Intel

T-Coffee has been updated to version 8.99. We added NetBLAST and some other helper utilities at the same time, so this version of T-Coffee has support for almost all of its various features. T-Coffee has a variety of excellent documentation including technical docs and a nice tutorial. Requested by Harrison Lab at Harvard Medical School.

VMD has been updated to version 1.9. There are a host of new features and updated plugins; details are available in the VMD release announcement. Requested by Jarrod Smith at the Vanderbilt Center for Structural Biology.

PHENIX has a new nightly release available: dev-780. It has the usual assortment of bug fixes and cutting edge features, so please try it out if you run into problems with the release version or want to preview the coming attractions. A partial list of changes in this version are in the PHENIX change log.

AUTO3DEM has been updated to version 4.01.10. This is a bug fix release. The AUTO3DEM homepage has manuals and release notes.

The CCP4 6.2.0 pre-release has been added to the tree. It contains bug fixes and the latest versions of many of the CCP4 tools (REFMAC, Phaser, et al), but it is missing a few things like ARP/wARP and documentation. Please try it out if you want to check out a new feature or encounter a bug in the current version, but also note that you are likely to find exciting new bugs in this version!

CMView is a new package for interactive protein contact map visualization and analysis. A manual, tutorial and FAQ are available on the CMView website.

breseq is another new package for SBGrid. breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. The manual and test data sets are available on the breseq website.

Bug Reports

xia2 had several bug reports over the last few weeks that are fixed by the latest update. Bug reports by Shiven Shandilya, Peter Zwart and Terry Lang.

There was a bug in the matplotlib installation available via Python in the /programs tree. Reported by Terry Lang at in the Alber Lab at UC-Berkeley.

The Schrodinger license server was inadvertently shut down due to a misconfiguration. Reported by Sabuj Pattanayek at Vanderbilt.

Thanks for your bug reports!

Published June 1, 2011