Dear Consortium Members and Affiliates,
We would like to welcome a new post-doctoral research fellow to the SBGrid team: Daniel O'Donovan joins us from the University of Cambridge where he worked on methods for the Bayesian analysis of NMR data with the CCPNMR project.
The update this month includes new versions of PHENIX, Rosetta, XPLOR-NIH, O, XDS, XIA2, Coot, MOSFLM and iMosflm and Lafire. We also updated quite a few packages used in EM including SPIDER, Bsoft, PFT3dr, IMOD and AUTO3DEM. There were also updates for the sequencing tools in the software suite including MUSCLE, CLUSTAL and Jalview as well as new packages for T-Coffee, PROBCONS, and MAFFT.
The Blobel Lab at Rockefeller University is our newest member!
The following software updates will be available tonight or tomorrow:
Linux and Mac OS X (PPC and Intel)
Rosetta has been updated to version 3.2. This version has full compatibility for use in the latest PHENIX. There is a new manual for this version. Requested by everybody.
XPLOR-NIH has been updated to version 2.27. There is a manual and an FAQ on the XPLOR-NIH website. Requested by the Chou Lab at Harvard Medical School.
Bsoft has been updated to version 1.7.0. Manual, howtos, workflows and demo data sets are available from the Bsoft website.
PFT3dr has been updated to work with Bsoft 1.7.0. PFT3dr website has some info.
IMOD has been updated to version 4.1.8. This new version can use your GPU to do reconstructions. More info on the IMOD website.
XIA2 has been updated to version 0.3.2.0. This version has full compatibility with the available versions of XDS. Docs and more on the XIA 2 home page. Requested by the Berkeley Center for Structural Biology at Lawrence Berkeley Labs.
MUSCLE has been updated to version 3.81. The developer has documentation and some benchamarks on the MUSCLE website.
Jalview has been updated to version 2.61. This update is mostly bugfixes. Release notes, documentation and an FAQ are available at jalview.org.
CLUSTAL has been updated to version 2.1. This includes updates for the clustalw command line tool and the clustalx graphical interface. Documentation, the change log and usual bits are online at clustal.org.
MAFFT is a new package for the software suite. Per the author "MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of less than about 200 sequences), FFT-NS-2 (fast; for alignment of less than about 10,000 sequences)." Version 6.846 is now installed. More info on the MAFFT website.
PROBCONS is another new addition to the software suite used for generating multiple alignments of protein sequences. The author claims it has the highest accuracy of all alignment tools to date using the BAliBASE benchmark. Version 1.12 is installed for all platforms. More information on the PROBCONS website.
T-Coffee is another new package in this update. T-Coffee is "a collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures." Fun! Read the docs at tcoffee.org.
OS X Intel and Linux
Coot has been updated to a recent development release, r3334. Requested by everyone.
SPIDER has been updated to version 19.00. There is extensive documentation on the SPIDER website at Wadsworth.
AUTO3DEM has been updated to version 4.01.3. The Baker Lab at UCSD has documentation, a tutorial and more on the AUTO3DEM website.
O has been updated to version 101022. The A-Z of O and the other bits are available on Alwyn Jones' website. Requested by members at Vanderbilt University.
Lafire has been updated to version 3.02 and it has shiny new graphical interface. The manual for the previous version is available on the Lafire website. Requested by members at Rice University.
XDS has been updated to 20101206. There is an FAQ and other documentation on the XDS website.
Coot on OS X Intel was breaking in strange ways after the last update. Cleaning up the shell environment for Python and tweaking some files in the installation resolved the problem. Shout outs to the half dozen members who reported it.
CNS was missing a library on OS X PowerPC. The CNS binary was recompiled semi-statically so it has no external dependencies for OS X PowerPC. Reported by Matt Whorton, MacKinnon Lab at Rockefeller University.
CNS was returning the incorrect platform type for the newish purely 64-bit OS X Intel machines. The getarch script was modified to support the new machines. Reported by Karl, Kevin and Andrew at UC Berkeley.
PHENIX and Coot were not playing together nicely if certain environmental variables were set. Local changes and an upstream change by the PHENIX developers resolved the problem. Reported by Engin Ozkan, Garcia Lab at Stanford.
XDS expired when the new year arrived. It was on the calendar, but we weren't around to see it. Jim Smith in the Fremont Lab at Washington University helpfully reminded us.
Thanks for your bug reports!