Dear Consortium Members and Affiliates,
Party people, what's up!? Here is your monthly SBGrid newsletter. Boston, along with most of North America, continues its unusually mild winter, but our European colleagues are making up for our lack of cold temperatures, wind and snow. Life really is like a box of chocolates...
We are happy to announce a new grid-enabled web application for performing Deformable Elastic Network refinements on low resolution structures. This web application, written by our very own Daniel O'Donovan, is highlighted in a recent Acta Crystallographica Section D paper. It is integrated with the SBGrid Science Portal and builds on the original DEN approach integrated into CNS by Gunnar Schroder and Axel Brunger. Big ups to Daniel, who will be leaving SBGrid shortly for the greener pastures of industry. Thanks Dan!
In related news, SBGrid has an open position for a scientific web developer. The role involves developing, updating and maintaining high-throughput structural biology work-flows in an academic environment. Existing, published SBGrid web applications have processed hundreds of structural biology problems utilizing hundreds of thousands of CPU hours through the Open Science Grid. The position includes developing new work-flows and applications in collaboration with academic researchers, as well as ensuring that the existing applications continue to serve SBGrid members. If you or someone you know might be interested, the complete position description is on our website.
Don't forget to join us on February 27th at 10:00am for an SBGrid Tea Break with Tim Stevens to hear more about CcpNmr SpecView and ChemBuild: the first next-generation CCPN software. More details are available on the SBGrid news page. CcpNmr ChemBuild is available as a new application this month.
For our Linux users Red Hat support for production use of Enterprise Linux 4 ends February 29, 2012. CentOS and Scientific Linux will also be ending production support for that version at the same time. If you haven't already updated your older workstations, it's a good time to do so. The list of SBGrid-supported operating systems and our support policy are available on our website.
Our scintillating scientific software update this month includes new versions of PyMOL, CcpNmr ChemBuild, Chimera, XDS, CNS, Xplor-NIH, AutoDock Vina, IMOD, EMBOSS, TiltPicker, Staden, GROMACS, Theseus, AMPS, MEAD, CPMGFit and a PHENIX nightly build as well as an exciting new GPU-accelerated molecular dynamics package called ACEMD.
Get down with your funky self!
Antonina Roll-Mecak is our latest member from the United States National Institutes of Health. She has a great looking lab website detailing her research interests, and she's also speaking at the upcoming Hybrid Methods conference.
The 6th International Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods will be held from March 14-18, 2012 in Lake Tahoe, California at the Granlibakken Conference Center. Several of the speakers are current SBGrid Consortium members, and a number of well-known structural biology software developers are speaking as well. Visit the conference website for more details.
The following software updates should be available today:
Linux and Mac OS X Intel
PyMOL has been updated to the 1.5 final release. Jason Vertrees and the Schrodinger developers have been hard at work on this lates release, and it boasts some ridiculous performance increases on modern graphics hardware. The PyMOL website has other release notes. Requested by everyone.
Chimera has been updated to the 1.6 release candidate. The long list of new features and fixed bugs is available in the Chimera release notes.
CcpNmr ChemBuild is a new graphical tool to construct chemical compound definitions for NMR. The ChemBuild website describes it as "especially created to handle concepts like protonation variants and magnetic equivalence which are required for NMR resonance assignment. Several different chemical file formats are supported, including PDB, .mol and .mol2, but ChemBuild is special in its ability read and write CCPN chemical component XML files." If this sounds useful to you, more details are available on the ChemBuild website, and the developer will be doing a webinar on February 27th.
CNS has been updated to 1.3 revision 7. This update includes revised and expanded tutorials on Deformable Elastic Network (DEN) refinement. The CNS website has all the documentation and input file preparation tools.
AutoDock Vina has been updated to version 1.1.2. This is mostly a bug fix release. Docs and more on the VINA website.
IMOD has been updated to version 4.3.4. There is a list of 4.3 changes as well as a list of the bug fixes in the point release. The IMOD website has a wealth of other information on this package for tomographic and 3D EM reconstruction. Requested by the Kornberg Lab at Stanford.
EMBOSS has been updated to version 6.4.0. Note that you'll need to download and configure local databases for use with EMBOSS. The EMBOSS website has all the details. Requested by the Harrison Lab at HMS.
XDS has been updated to the latest bug fix release. It's the same package that we updated to in January with one small bug fix. The XDS website has documentation and a change log. Are you using or interested in using XDS on a cluster? We want to figure out the best way to package XDS for our cluster users, so please send an email to firstname.lastname@example.org if you want to be part of the test group for any new cluster configuration options for XDS.
Staden has been updated to version 2.0.0b9. This is the first updated in almost 8 years, and it's still a beta with some rough edges. The Staden website has a user manual and a description of the new features. Please let us know if you encounter any problems!
GROMACS has been updated to version 4.5.5, and the OS X and 64-bit Linux builds have full MPI support. The GROMACS manual has information on how to run this free molecular dynamics tool. The complete release notes are also online.
NMR relax has been updated to version 1.3.13. This update should resolve any problems people have seen with the software on 64-bit linux machines. The relax website has the usual things. Note that this version includes some syntax changes for how files are read. Please see the relax PDF documentation for more information. Requested by Chazin Lab at Vanderbilt University.
Theseus has been updated to version 1.6.2. Theseus is a tool for superimposing multiple macromolecular structures. The Theseus website has documentation as well as an explanation of why its maximum likelihood method is more accurate than the conventional least-squares approach.
AMPS has been updated to version 2.3a. This is a final bug fix release as the package has not been updated since 2004. AMPS is the venerable suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching from Geoff Barton's lab at the University of Dundee.
MEAD has been updated to version 2.2.9. This was a catch up release for an older package that includes some bug fixes and a change to an open source license. There is a MEAD manual PDF online.
CPMGFit has been updated to version 1.43. This is a bug fix release. The CPMGFit manual is online.
ACEMD is a new package for molecular dynamics. It features a heavily optimized engine specially designed to run on NVIDA GPUs. ACEMD is extremely fast (115ns/day for DHFR using 1 GPU) and allows performing MD simulations on the microsecond scale on a single workstation. ACEMD is a fully featured platform (PME, NPT, NVT, TCL, PLUMED, CAMSHIFT) that can read CHARMM/NAMD and AMBER input files. This single-GPU version is free for academics and non-profits. More information is available on the Acellera website.
TiltPicker has been updated to version version 2.0b13. TiltPicker is a graphical user interface for picking particles from image tilt pairs for such applications as random conical tilt (RCT) and orthogonal tilt reconstruction (OTR). The TiltPicker web page has some additional details.
The EMAN2 installation had a number of small bugs uncovered when people tried to run their own python scripts using the EMAN2 python modules. We fixed a number of integration bugs and are also including an 'e2python' wrapper script that can be used to run python scripts that want to use the EMAN2 modules. Reported by Claudio Ciferri in the Settembre Research group at Novartis and Katerina Toropova in the Leschziner Lab at Harvard.
The 64-bit Linux installation of Python is built with the high performance Intel compilers and linked against the Intel Math Kernel Libraries for best performance when using the NumPy and SciPy modules, and we had some missing linked libraries. These should all be fixed, and the 2.7.2 Python installation in the x86_64-linux branch should be working for everyone. Reported by Sarah Soss at Vanderbilt University.
The Bourne shell syntax initialization files had a few small bugs when used with Zsh. We have tweaked the shell set up to accomodate our Zsh shell users. Reported by Robert Campbell at Queens University.
The ATSAS package had some problems with the DAMAVER pipeline when running under OS X. We re-jiggered our wrapper scripts and symlinks that make the package work to fix the problem. Reported by Anamika Patel in the Cosgrove Lab at SUNY Upstate.
The Xplot84 display tool included with CCP4 was not able to display some plots under OS X. The driver was updated with an older version to resolve the issue! Reported by Isabel Garcia-Saez at IBS Grenoble.
ROSETTA on OS X Intel was linked against some missing libraries. We rebuilt the package to resolve the linkage issues. Reported by Patricia Amara at IBS Grenoble.
Modeller 9.10 had some 32/64-bit mismatch issues with its bundled libraries. We fixed the problem by forcing the software to prefer its 32-bit libraries and reported the issue to the developers. Reported by Axel Brunger at Stanford.
Thanks for your bug reports!