Dear Consortium Members and Affiliates,
Good afternoon, sports fans! The May SBGrid update is here, and we are also hosting a workshop on centrifugation hosted by Borries Demeler of Ultrascan fame.
This software update includes new versions of IMOD, MODELLER, nuccyl, CCP4mg, PHENIX, Coot, Lafire, NMRViewJ, PHYLIP, XPLOR-NIH, and Schrodinger. Two new software titles for this month are saxsview and ESPript.
Centrifugation Workshop
The SBGrid Consortium and NSF RCN would like to invite you to a Centrifugation Workshop to be held at Harvard Medical School:
"Structure-function studies using analytical ultracentrifugation, and the UltraScan data analysis suite"
Dr. Borries Demeler, Associate Professor of Biochemistry The University of Texas Health Science Center at San Antonio
Friday, May 20, 2011 9:30am-5:00pm Countway Library, Room 403, Harvard Medical School 10 Shattuck St, Boston, MA 02115
Hosted by: Piotr Sliz
Registration required ($85/pp including lunch) Registration spaces are limited and will be reserved on a first come/first served basis. To register to please go to the event page
Description:
In this workshop Dr. Demeler will provide an overview of the analytical ultracentrifugation technique. This workshop will be of interest to structural biologists, biochemists and biophysicists interested in solution characterization of macromolecules, their interactions and assemblies. During the workshop Dr. Demeler will review the background of sedimentation velocity experiments, discuss the observable parameters, the types of data collected, and the modelling approaches used for extracting molecular parameters from the data. Using tools in UltraScan, he will demonstrate the entire workflow from experimental design to data management, modelling and optimization, visualization and reporting. He will demonstrate the software using several representative examples, using both the UltraScan GUI application and the UltraScan LIMS system, a web-based MySQL database, and the TeraGrid Science Gateway portal for UltraScan. Dr. Demeler will then discuss the SoMo (Solution Modeler) rigid body bead modelling suite, its relevance to X-ray and NMR experiments, and conclude with perspectives of developments currently underway in our laboratory.
For questions regarding this workshop, please contact the SBGrid consortium at events@sbgrid.org.
Software Updates
Linux and Mac OS X (PPC and Intel)
IMOD is now at version 4.1.9. This is a bugfix release, with a number of bugs resolved. More information is available at IMOD's website.
MODELLER version 9.9 is now available. More information about this release is at their website.
nuccyl is now at 1.5.2. This release fixes a bug involving nucleic acids and adds chain name information to the name created with the "nuccyl -cyl_3" command. nuccyl's website has the usual info.
PHYLIP version 3.69 is now in the SBGrid distribution. You can find more information on PHYLIP's site.
ICCB Libraries have been updated to the newest version. ICCB's website provides more data on the libraries and screening.
Linux and OS X Intel
saxsview is a new addition to the SBGrid distribution at version 0.2. The program can read, convert, and view 1D and 2D Small Angle X-ray Scattering (SAXS) files. Check the project's website for documentation.
CCP4mg 2.5.0 is now out. This is a fairly major update, with numerous bugfixes and enhancements. Documentation and more is available at the CCP4mg website.
PHENIX is at 1.7.1, a new release. This has a large number of improvements over the 1.7.0 release, including new commands, new GUIs, and refinements to existing commands. You can find more information about the release through PHENIX's website.
Coot is updated to revision 3468 on Linux and revision 3450 on OS X. This is another pre-release build, and has the usual amount of bugfixes and revisions. The OS X version now has the ability to use Kevin Keating's RCrane extension. Documentation and information is on Coot's website.
PyMOL is now at version 1.4.1. This is a minor fix over version 1.4 which solves its compatability problems, and is now the default. Schrodinger has more information on PyMOL's site
Lafire is now at 3.5. Go to Lafire's website for more information.
NMRViewJ has hit version 8, and we have 8.0.3. This is the last free release, and NMRView's site has more on the software and the license change.
EM-BFACTOR is a new addition to the SBGrid software tree. According to its authors, it "allows sharpening of high resolution information in 3D maps obtained by electron cryomicroscopy". Could be useful! Head over to EM-BFACTOR's web page for more information.
XPLOR-NIH version 2.28 is now available. This release adds many improvements to the package, including a number of bugfixes and parallel calculation performance increases. The website has more documentation.
Aqua version 3.2 is now also on Intel Macs. This is the same version as the Linux copy we've provided for a while. The software's website has explanations and documentation.
Linux
ESPript is a new package for SBGrid. It generates PostScript from aligned sequences, automatically colored according to their degree of similarity. The website has documentation and tutorials.
Schrodinger is now at the 2011 release. This version adds a number of improvements, including performance increases, enhanced graphics and usability, and support for GPGPU. Schrodinger's site contains further documentation.
Bug Reports
SPIDER had a number of bugs recently, all involving the web and jweb tools. They should all be resolved now, and thanks to Fred Metoz at IBS, Berith Isaac at MCB, and Edward Eng at IDI for all pointing out separate issues.
XDS-Viewer on OS X was crashing due to a missing Qt version, which is now fixed. Thanks to Fred Metoz again for telling us.
HKL2000 didn't work on OS X 10.5 due to a compatibility issue. We got a new, fixed, binary from HKL software that adds 10.5 compatibility. Credit goes to Stephen Long at MSKCC for finding this bug.
XIA2 on Linux accidentally used a system binary called "truncate" instead of the CCP4 program when the former existed. It will now always use the CCP4 truncate. Terry Lang and Andrew Ring at Berkeley get the bug-squashing points on this one.
Thanks to everyone who reports bugs for helping us make SBGrid better.