Dear Consortium Members and Affiliates,â€¨
Software updates will be sent to your site tonight, Wednesday, June 20. This month, you will be receiving updates for the EM applications Bsoft, Frealign, 2dx, and Web. For crystallographers, we have a MacIntel version of HKL2000, and we also add an older application for viewing X-ray diffraction images – adxv. For the general audience, we will add a new release of Pymol.
Immediately after receiving the software updates tonight, you will be using the newest installed versions. If there are any problems, please report them (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). â€¨â€¨
Please continue reading for full details.
Piotr Sliz, Ph.D.â€¨
Group Leader, Structural Biology Computing Group, SBGrid
Ben Eisenbraun, the SBGrid Scientific Programmer, attended the Apple Worldwide Developers Conference in San Francisco this past week. Ben presented a poster detailing SBGrid’s use of Apple technologies for compiling and maintaining structural biology applications and grid computing. Additionally, Ben attended numerous developer sessions to be able to advance our abilities to harness the power of OS X for structural biology applications.
Apple Design Award:
- The application Papers won the Apple Design Award in the science category. Papers is a affordable reference manager with an iTunes like interface and integrated connectivity to PubMed resources.
SBGrid and Apple's New Operating System:
- Leopard (Mac OS 10.5) release is projected for early fall; several new features of the new operating system were highlighted during the conference. SBGrid already has access to the beta release and will start to compile structural biology applications for the new release soon.
In Fedora Core 6, the default PDF viewer is no longer Gpdf. In order to open a PDF from a command line, type evince sample.pdf. Why evince instead of Gpdf? Evince was written to replace the multiple document viewers in GNOME, replacing them with one simple application.The following software updates will be available later tonight:
Linux and Mac OS X (PPC and Intel)
Bsoft will be upgraded from 1.3 to 1.4. Sevelar minor changes are included in the new release. Extra capability includes picking boxed particles along filaments and searching for point group symmetry.
Adxv 1.93, a program to display x-ray diffraction images, will be added to the distribution. This is a new program whose main function is to display protein crystallography XRD data. It allows for both 2D and 3D display of data. Information and instructions can be found on the Adxv website.
Linux and Mac Intel Only
Frealign – a single particle reconstruction program developed at Brandeis University by Niko Grigorieff – will be upgraded from version 7.05 to 7.07. This new release includes minor bug fixes and provides more verbose log files.
Web, a viewer for another EM application, SPIDER, now runs from a wrapper script to fix color-depth issues in Intel and PPC Mac branches. Since Web requires an 8-bit xserver to display, the new script fires up an 8-bit server, starts xquartz window manager and runs web, and then cleans up gracefully once you exit.
Pymol will be upgraded to release candidate 10 (SBGrid Build -- 0.99rc10). This release should resolve some crash issues members were experiencing with 0.99rc8. Other minor changes that come along with this release are noted in the CHANGE file in your …/pymol/0.99rc10 directory.
Additional Platform Availability
2dx 2.1.0, previously only available for PPC Mac, will now be available for Linux and Intel Mac branches.
HKL2000 will now be available for the Intel Mac branch for those members who have separately purchased a license for this program.