The following bugs have been fixed since the last newsletter:
CNS 1.1 was segfaulting on OS X Intel and the cns_solve_env script had some syntax errors for modern OS X versions. I rebuilt the executable and patched the set up script. Bug report and fixes suggested by David Gohara in the Di Cera Lab at St. Louis School of Medicine.
The integration between PHENIX and Coot was broken on 32-bit linux platforms. A new Coot build resolved the issue. Reported by John Williams, Williams Lab at City of Hope.
Dear Consortium Members and Affiliates,
Aloha means hello and goodbye, so aloha. It's a quiet month for news. We have a small contingent of CCP4 developers coming to visit July 30th, but we haven't really worked out the details. We hope to cajole them into giving some lightning talks on the latest and greatest CCP4 bits. We'll have more information as we get closer to the date.
We have an update planned for today that we started pushing out last night and should already be available at some sites. Today's update includes new versions of PHENIX, Jalview, MODELLER, BALBES, and BioPython as well as two new packages: Elves and UROX.
Aloha!
We are pleased to welcome three new members from Washington University in St. Louis: Tom Brett, Niraj Tolia and Joe Jez.
The following software updates will be available tonight or tomorrow:
Linux and Mac OS X (PPC and Intel)
PHENIX has been updated to version 1.6.2-432. Documentation and a change log are available. Requested by everyone.
Jalview has been updated to version 2.5. Documentation is online. Requested by the Garcia Lab at Stanford. (Yes, I know they just released 2.5.1 this morning. Them's the breaks.)
MODELLER has been updated to version 9v8. The MODELLER website has a documentation page. Another request from the Garcia Lab.
BALBES version 1.0.0 has been installed into CCP4 across all active branches. There is a BALBES manual. Requested by the Jeruzalmi Lab at Harvard University.
BioPython has been updated to verison 1.5.4. Release notes and more are on the BioPython website. Requested by the Alber Lab at Berkeley.
James Holton's Elves is a new application for the SBGrid software suite. There is a manual, which you are not supposed to read, on the Elves website. Requested by the Berger Lab at Berkeley.
Linux
UROX version 2.0.2 is a new package for the linux branch. UROX is designed for interactive fitting of high-resolution models obtained by X-Ray crystallography into Electron Microscopy reconstructions. It can also be used to fit two maps together (e.g., in tomography), or to perform Normal-modes calculations. Documentation and a few other bits are available on the UROX website. Requested by Gonen Lab at the University of Washington.
Aloha means hello and goodbye, so aloha. It's a quiet month for news. We have a small contingent of CCP4 developers coming to visit July 30th, but we haven't really worked out the details. We hope to cajole them into giving some lightning talks on the latest and greatest CCP4 bits. We'll have more information as we get closer to the date.
We have an update planned for today that we started pushing out last night and should already be available at some sites. Today's update includes new versions of PHENIX, Jalview, MODELLER, BALBES, and BioPython as well as two new packages: Elves and UROX.
Aloha! With his usual flair for the incomplete, Piotrek informs us that we'll be graced by the presence of some of the CCP4 developers. I have no idea which ones, but we hope to twist their arms a bit to give a talk here at HMS about the latest and greatest developments in the world of CCP4. We're pleased to report that we've secured competitive pricing on two Linux-compatible workstations from our new preferred hardware vendor, ThinkMate. We're working with ThinkMate because they do a fantastic job with high-quality system builds and because they ensure that each system they build enjoys full Linux compatibility. All systems come with a 3 year warranty and can come pre-installed with CentOS, SBGrid's recommended linux distribution.
The workstation configurations are available at thinkmate.com. The SBGrid Standard Workstation comes with a quad-core CPU, 3GB of RAM and an NVIDIA Quadro FX 380 graphics card ($1173). The SBGrid Pro Workstation has a default configuration with two quad-core CPUs, 6GB of RAM and an NVIDIA Quadro FX 580 graphics card ($2123). The Pro Workstation can also serve as a small file server, accommodating up to 8 hot-swap hard drives paired with a 3ware RAID card.
If you have any questions about the configurations, please email us or feel free to contact our ThinkMate sales representative Jon Breen at 800-371-1212 x4249 or via email at jon.breen@thinkmate.com. Please note that we don't receive any sort of compensation from these sales -- we work on these configurations solely for the benefit of our community.