Just testing the newsletter.
Dear Consortium Members and Affiliates,
I am happy to announce that we received a five-year support grant from the National Science Foundation to further develop SBGrid. Additional funding will allow us to hire a programmer that will adapt a number of structural biology applications to utilize grid-computing resources. As an NSF Research Coordination Network we will also offer three outreach programs mostly focused on exposing high-school and college students to grid and high performance computing technologies. I would like to thank all PIs that provided us with letters of support.
SAVE THE DATE! The first SBGrid user summit ‘Quo Vadis Structural Biology?’ will take place on May 5th and 6th 2008 in Boston, MA. We will have a number of talks and workshops focused on structural biology computing. More details will be provided next month.
I wanted to remind you that as an SBGrid Consortium member you are entitled to submit a general user proposal for cluster/grid computing access
Our software push is scheduled for tonight. Please take a few minutes on Thursday to test if your major applications are working well. Our staff will be on call tomorrow to resolve any urgent issues. In addition, in our ‘hints, tips and tricks section’, we provide an example of how to change your configuration to use an older version of an application. This can often work as a quick fix to your problems. This month we have updates for MrBUMP, NMRPipe, Swiss PDB Viewer, HKL2000, Raster3d and Xia2.
If there are any problems, please report them at <http://www.sbgrid.org/bugs>. You can always switch to an older version of the application while we work on your request—just use ‘sbgrid –n’ for more information. Many of these monthly updates and additions are prompted by member requests, so please do not hesitate to request new applications <http://www.sbgrid.org/req>.
Piotr Sliz, Ph.D.
Structural Biology Grid (SBGrid)
NSF Research Coordination Network
Gan-Guang Liou from the National Health Research Institutes in Taiwan, and Colin Parrish at Cornell University.
Hints, Tips and Tricks
One of the features of our software distribution model is that we can concurrently support multiple versions of the same program. If an update causes a problem at your site, you can override the default version of any program by creating a text filed named .sbgrid (dot-sbgrid) and placing it in your home directory. When the programs are initialized by the shell, the process checks that file for version overrides. So if the default version of Coot is 0.3.3, and you would like to run the previous version in Linux, use this line in your ~/.sbgrid file:
setenv COOT_L 0.3.1
The exact line will be slightly different depending on your OS (Mac or Linux) and the name of the program. (E.g. COOT_M on Macintosh computers.)
Stereo Capable Macs
While we have had stereo capabilities on our Linux workstations for quite some time, until recently, we weren't able to evaluate, test and troubleshoot stereo problems on OS X. This has changed with the addition of a stereo-capable PowerPC Macintosh this month. We have also placed an order for a stereo-capable Intel Mac, so by the end of August, we should be in a good position to test stereo applications on OS X as well as assist in resolving any issues you might encounter.
The following software updates will be available later tonight:
Linux and Mac OS X (PPC and Intel)
MrBUMP has been updated to version 0.4.0.
NMRPIPE will be upgraded for Linux and OS X PPC and will be available for the first time on Intel Macs. This is an update to version 2007.030.16.06 which was released in July and is available in the programs tree as version 2007. NMRPIPE provides comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. As we were running a version from 2005 prior to this update, there are too many new features to mention. See <http://spin.niddk.nih.gov/NMRPipe> for more details.
SPDBV, the Swiss PDB Viewer, has been updated to the latest release for all platforms. For OS X, this is release 3.9b2 and for Linux it is 3.7sp5. This was updated in response to a user request.
HKL2000 has been upgraded to version 2000.0.98.698d. This new version supports ASDC q-270 and MAR CCD 300 detectors.
RASTER3d has been upgraded to version 2.7d. This is primarily a bug-fix release to resolve issues with TIFF output on older Fedora and Redhat releases.
OS X PowerPC Only
XIA2 is officially available for PowerPC Macs at version 0.2.6.0. This is an application we offered in the July update for Linux and Intel Macs that was delayed while we worked with the developer, Graeme Winter, to resolve a bug in the PowerPC build. Xia2 is a new system which quickly reduces raw diffraction data. This reduced data can be input into a phasing program to start finding the structure. Full details can be found on the Xia2 website <http://www.ccp4.ac.uk/xia/>