Dear Consortium Members and Affiliates,
Just in time for the holidays, we have a large monthly update for you. Harvard Medical School's generous holiday policy means that SBGrid staff will be out of the office between Christmas and New Years. We'll be watching for emergencies, but general operations will be mostly suspended during this period. Please plan accordingly.
Through a special agreement with Schrödinger, we are pleased to provide Maestro and PrimeX to all SBGrid members. Schrödinger's powerful molecular rendering and visualization application, Maestro, is available to all academic researchers at no charge. Maestro is the front-end GUI to all SchrÃ¶dinger computational modules, and can be used to view, analyze, and manage calculated results. In addition, Maestro generates publication-quality molecular graphics suitable for illustrations and presentations.
Schrödinger has also recently made available at no charge to academic users PrimeX, a comprehensive package for protein crystal structure refinement. PrimeX is fully integrated with Maestro, which provides an easy-to-use graphical interface for setting up complex computations. This time-limited offer runs from now until June 30, 2009, and is intended to introduce PrimeX to the academic user community.
Both Maestro and PrimeX are available in the Linux branch and are pre-configured to obtain licenses from the SBGrid licensing server, so there should be no special set up required on your part.
The update this month includes new versions of CCP4, ARP/wARP, Phaser, Amber, XDS, NMRViewJ and Curves, as well as new installations of Maestro, PrimeX, Protomo, NMR Relax, Imosflm and em2em. This update weighs in at 4-7 gigabytes depending on which branches your site is currently receiving, and we expect it to take at least 24 hours to get out to all sites, so while the update is starting tonight, your site may not have the new programs in place until Friday.
As an additional note, the total size of the distribution for a site receiving Linux, IRIX and both OS X branches is not quite 100 GB. Our recommendation for several years was to host the programs installation on a 60 to 80 GB volume, but our current recommendation is to use a 250 GB volume to allow for future expansion.
The following software updates will be available later soon:
Linux and Mac OS X (PPC and Intel)
CCP4 has been updated to version 6.1. This version includes updates and bugfixes for virtually every CCP4-related package including refmac, Phaser, Buccaneer, MrBUMP, pointless, RAPPER, Scala, MOLREP and more. Along with this update, the latest CCP4i interface for Phaser 2.1.4. ARP/wARP 7.0.1 has also been installed. More details on this new CCP4 release can be found on the CCP4 website.
Curves version 5.3 is a new installation for Linux and OS X Intel and gets a refresh for OS X PowerPC. Curves provides an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis. Documentation and usage notes are available on the Curves website.
XDS has been updated to the September 10, 2008 release. There a few new features listed in the release notes, but this update is mostly to replace the binaries set to expire on December 31st.
NMRViewJ has been updated to version 8.0.a27. More details are available on the NMRViewJ website.
Relax is a new package designed for the study of the dynamics of proteins or other macromolecules though the analysis of NMR relaxation data. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, and the Lipari and Szabo model-free analysis. A full feature list and documentation can be found on the relax website.
Linux and Mac OS X Intel only
For Harvard and affiliates, the Amber Molecular Dynamics package has been updated to version 10. This build includes Amber Tools version 1.2. Due to the Amber licensing requirements, we are not able to provide this package to all members. License prices are very reasonable, and we're happy to help you get the software running if you purchase a license for your institution. Visit the AmberMD home page for documentation and licensing details.
Mac OS X Intel and PowerPC
Imosflm version 1.0.0 is a new installation for the OS X branches. The 1.0.0 release has almost all the functionality of the old X11 based ipmosflm GUI. Documentation, including a tutorial and the full guide, are on the iMosflm website.
The Protomo package for electron tomography of thin specimens is a new install at version 1.1.3. The available documention is at /programs/i386-linux/protomo/1.1.3/doc.
PyNMR is a new plugin for the Linux version of PyMOL. Click the Plugin menu and choose NMR Extension and then Help in the new window for the available documentation.