Dear Consortium Members and Affiliates,
This is a short newsletter befitting of a small update. We have new versions of Coot, PHENIX, CCPNMR, NMR relax, and BLAST in this update, as well as a few new packages including BioPython, PROFphd and SAM.
Harvard mostly shuts down for the week between Christmas and New Years, so while we will sporadically be checking email and on the alert for emergencies, we are out of the office next week. Please try not to break things. Thanks!
Happy Holidays to you and yours!
The following software updates will be available today:
Linux and Mac OS X (PPC and Intel)
Coot 0.6 has been released, and the software suite has been updated to include this version. We are also including a 64-bit build of Coot on linux for the first time. This 64-bit build is available for machines running Fedora 6+ and CentOS/Red Hat 5. There are extensive resources to help you get started with Coot including the manual, FAQ, a couple tutorials and the Coot page on the CCP4 wiki.
PHENIX nightly build version dev-256 has been installed. It is not set as the default version. You can enable it by using a ~/.sbgrid file. There is updated documentation for the nightly build on the PHENIX website.
CCPNMR has been updated to version 2.1.2. The CCPNMR website has lots of resources for getting started with this powerful NMR software.
BioPython is a new addition to the Python 2.5.2 installations in the software suite. The tutorial and cookbook contain many examples on how to use the software.
PROFphd is a new package added as part of the pipeline to create fragments for Rosetta. There's not very much documentation on it.
Linux and Mac OS X Intel
SAM, the Sequence Alignment and Modeling System, is a new package in the software suite. SAM is a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. There is a manual on the SAM website.
We are pleased to welcome the DiCera Lab as our newest member.
Aline can use Muscle, CLUSTALW and DSSP for preparing figures, but it was missing the correct path set up to do so. The paths were fixed, and Aline now correctly finds and uses the helper software. Reported by Elton Zeqiraj in the Sicheri Lab.
The standalone version of LABELIT was dumping Python errors for some of its commands. Since LABELIT has been included with PHENIX since the official 1.5-2 release, the standalone LABELIT was removed from the software suite in favor of the bundled version. Reported by Daqi Tu in the Eck Lab.
REFMAC versions 5.5.099 to around 5.5.102 all had problems with alternate conformations that would result in bogus refinement results. Both the linux and OS X Intel versions of REFMAC have been updated, but the OS X PowerPC branch is still running an older version. The updated REFMAC for OS X Intel is a 10.5+ only binary, so 10.4 machines will continue to have problems with alternate conformations. Reported by John Pascal, Pascal Lab and Frederic Metoz, IBS-Grenoble.
Frealign version 7.05 on linux had some broken symlinks in its installation directory which were relinked against the proper files. Reported by Zongli Li in the Walz Lab.