Dear Consortium Members and Affiliates,
This is a small update to get out some fixed packages and updates to a few existing ones. We have a bunch more in the pipeline, so don't fret if your favorite application isn't on the list. Software on the update list includes PHENIX, XPLOR-NIH, Gnuplot, Frealign, the Grigorieff EM utilities, NAMD and Coot.
Here's hoping you are having a lovely summer.
The following software updates will be available tonight or tomorrow:
Linux and Mac OS X (PPC and Intel)
Gnuplot has been downgraded to version 4.2.6 as the default. The 4.4.0 version is still available in the software tree, but it is not as compatible with most of the current scientific software as the older version. This should resolve problems with ATSAS output (and a few others).
Frealign has been updated to version 8.09, and we now have the multi-processor builds for multi-core reconstructions. Niko Grigorieff has set up a nice web forum for questions about using his software. Requested by the Harrison Lab at HMS.
The Grigorieff tools (CTFtilt, CTFfind, Bfactor, etc) have all been updated to their latest versions, and we are now including the multi-processor builds where available. Requested by the Raunser Lab at MPI-Dortmund.
CNS version 1.3, which was introduced last month, has had a few bug fixes courtesy of Axel Brunger.
NAMD has been updated to version 2.7b3. The NAMD website has release notes, documentation, an FAQ and a wiki with tips and tricks for running your very own molecular dynamics simulations.
OS X Intel and PowerPC
Coot has been updated for both OS X platforms to Subversion revision 3065. This will hopefully resolve some outstanding Coot bugs for OS X, so please try it out.
The following bugs have been fixed since the last newsletter:
CCP4 on OS X PowerPC was linked against some older versions of the IBM compiler libraries and was failing. Updating the libraries resolved the problem. Reported by Matt Whorton, MacKinnon Lab at Rockefeller University.
The CNS 1.3 builds, including the CNS utilities, were rebuilt to support all of our supported operating systems. Bug reports from Sabuj Pattanayek at Vanderbilt University and Hisae Matsuura in the Jardetzky Lab at Stanford.
EMAN version 1.9 in the i386-mac branch was using the environment Python, but it was compiled with the OS X system python. It was updated to use the system python, and a version supporting OS X 10.6 was added to the tree. Reported by Albert Weixlbaumer, Darst Lab at Rockefeller University.
The OMP_STACKSIZE environmental setting in place for CNS can conflict with the BUSTER command line utility. Unsetting the environmental variable in your local environment resolves the problem with BUSTER. Reported by Dave Bushnell from the Kornberg Lab at Stanford.
Thanks for your bug reports!