Dear Consortium Members and Affiliates,
We have a nice update for you today that includes new versions of Coot, CCP4mg, PHENIX, VMD, Situs, CCPNMR, MOSFLM and iMosflm as well as HKL2000. In update pipeline, we have CCP4 6.1.2, Bsoft and PFT3DR, Frealign, PyMOL and some general utilities including Gnuplot, the statistics package R and Xfig/Transfig. We'll shoot for September 1st for the next official update.
If you have any comments about the update or suggestions for new applications, please feel free to share them with other members of the SBGrid community. Send email to email@example.com.
Linux and Mac OS X (PPC and Intel)
Coot has been updated to revision 0.6-pre-1-revision-2172 for OS X and revision 2185 for linux. Both of these revisions include support for the Zalman stereo 3d LCD. The change log available on Google Code is the best way to find out what's new. Requested by Peersen Lab at Colorado State.
CCP4mg has been updated to version 1.111.0. This is a bug fix release with few new features. If you haven't tried CCP4mg since they moved to the new Qt interface, you should check it out. It's much faster and includes some nice wizards for generating movies and preparing images. Requested by the Sliz Lab at Harvard Medical School.
The PHENIX nightly build has been updated to version 1.4-125. PHENIX and Coot are two packages that I'm trying to update at least once per month to keep up with the rapid development pace. You can choose to always use the latest nightly version by adding a line like 'setenv PHENIX_L nightly' or 'setenv PHENIX_M nightly' to your ~/.sbgrid file. Requested by the Springer Lab at the Immune Disease Institute.
VMD has been updated to version 1.8.7. This new release includes 32 and 64-bit versions for linux, and both the linux and OS X releases also support CUDA for GPU accelerated calculations. The developers noted that by using CUDA, "typical acceleration factors for the algorithms in VMD are: electrostatics 22x to 44x, implicit ligand sampling 20x to 30x, molecular orbital calculation 100x to 120x." Release notes and additional information are available on the VMD website. Requested by the Peersen Lab.
Situs has been updated to version 2.5. This is the 10th anniversary release, and it includes an extensive list of new features. Requested by the Jeruzalmi Lab at Harvard University.
CCPNMR has been updated to version 2.0.7. The CCPNMR software suite is a series of programs for macromolecular NMR spectroscopy integrated with the CCP data model designed with the the intention to provide one suite of programs to carry out all tasks needed in macromolecular NMR spectroscopy. Additional information including CCPNMR documentation can be found on their website. Requested by the Selenko Lab at the Leibniz Institute for Molecular Pharmacology.
MOSFLM and iMosflm have been updated to their latest versions (7.0.5 and 1.0.3 respectively). Details on the new features are available in the release email. Requested by the Springer Lab.
HKL2000 has been updated to version 2000.0.98.699a. This update includes a small change to the configuration. If you have a directory at ~/hklint with detector definitions, that directory will be set in your shell environment. If there is no directory there, then HKL2000 will use its built-in default setting of /usr/local/hklint. If you'd prefer to not use either of these directories, then you can add your own HKLINT setting after sourcing /programs/labcshrc. Requested by the Peersen Lab.
The sync scripts which keep each site updated had a bug in the rsync command line options which only manifested itself with clients running rsync version 3.x. Discovered and reported by Ã–zkan Yildiz at the Max Planck Institute in Frankfurt.
SPOCK requires a license to be present in the installation directory in order to run, and it has to licensed on per-lab basis. In order to make this work for everyone in the consortium, we have added a symlink from the SPOCK directory to /usr/local/share/LICENSE.spock, which will allow you to install your own license while using the provided SPOCK binaries. Problem reported by Xiang Xu from the Furie Lab at Beth Israel Deaconess Medical Center.
DelPhi was broken on both OS X platforms, since it was initially compiled and installed for OS X 10.3. The program has been rebuilt to run on OS X 10.4 and 10.5, Intel and PowerPC. Reported by Sam Cross in the MacKinnon Lab at Rockefeller University.
Coot for OS X PowerPC linked against a G5-optimized version of libgmp, which was unable to run on G4s. The library was rebuilt to support both G4 and G5 clients. Reported by Jason Wells at the City of Hope Beckman Research Institute.
Thanks for your bug reports!