Dear Consortium Members and Affiliates,
As summer slides away we are gearing up for a new academic season and sending along our August news. We've got an answer to a common SBGrid Data Bank question, the webinar line-up for the next few months, details on our next SBGrid-Schrodinger Working Group, a software release with 9 updates and 2 new applications, and 3 member publications highlights.
Many of our members have asked "why do I need to deposit data in the SBGrid Data Bank if I have already made a deposit in the PDB?" The answer: the SBGrid Data Bank does not replace the PDB, but performs a different, complementary function. The PDB stores structural models and structure factor amplitudes. The SBGrid Data Bank stores primary diffraction data sets (images), which the PDB does not collect and for which there is no common repository currently available. We've added a brief FAQ to our website to answer this and other common questions.
Please note that we accept datasets for all publications - new and old. Thank you to all that have already made deposits!
We've just set the dates for our next round of webinars and will kick things off in September with a presentation from Alexandre Bonvin on "Modelling biomolecular complexes using HADDOCK: local vs server mode". Webinars are held on Tuesdays at 12pm. Please mark your calendar for this and other upcoming dates:
- September 8th: HADDOCK with Alexandre Bonvin
- September 22nd: Phenix/DIvCon plugin with Lance Westerhoff
- November 17th: DIALS with Graeme Winter
- December 1st : ProDy Python Module with Ivet Bahar
Our next SBGrid-Schrodinger Working Group will focus on Molecular Dynamics. Dmitry Lupyan will present and we are asking that users complete a tutorial prior to the presentation to make the most of our time with Dmitry. The tutorial and additional details will be sent separately to those that signed up to take part in the working group last month. If you have not signed up, you can still do so by completing our Google form.
For our August Tale we heard from James Berger, who recently made the move from UC Berkeley to Johns Hopkins where he is balancing his efforts to understand the DNA replication system, his interest in bridging the gap between structural biology and physics, and new opportunities to work closely with clinicians. Be sure to read the full story.
If you have submitted DEN or WSMR jobs to the SBGrid Science Portal, we apologize for any delays you are experiencing. We've had some network problems when connecting to the OSG and some buggy configuration issues on our end. If your job is urgent, please contact us at email@example.com and we will try to give it priority.
The software update for the month of August includes new releases for autoPROC, BioXTAS RAW, BUSTER, CCP4, EMAN2, HKL2MAP, Modeller, UltraScan III, and xmipp. We've also added two new applications to the SBGrid tree: DoGpicker and Scipion.
SBGrid member labs published over 42 manuscripts during the last month, a full listing of which can be found on the Member Publications page of the SBGrid website. Here are some notable highlights:
- Axel Brunger's laboratory at Stanford report on synaptotagmin-SNARE machinery based on structures partially determined with diffraction data from an X-ray free-electron laser. Read their recent Nature publication for more details.
- From Frank Sicheri's group at the University of Toronto comes new insight into the baculovirus protein PK2, its inhibitory properties and link to improved baculovirus fitness. Read the full story in PNAS.
- A new review on DNA methylation pathways, from Dinshaw Patel at Memorial Sloan-Kettering, was published in Nature Review Molecular Cell Biology. Check out the Aug 21st edition for more.
autoPROC was updated to version 20150812. This update represents a big jump up from version 1.0.2. You'll notice a number of improvements including a new feature that allows visualization of images and predictions and new scaling options when using "pure" AIMLESS-only or XSCALE-only paths within autoPROC. Full details are in the Release Notes of your installation.
BUSTER's newest version is 20150812. This release includes improvements to the buster-report, options for more control over geometry analysis, and the ability to run multiple input models in Pipedream. Check the Release Notes in your installation for a full list of changes.
Please Note: autoPROC and BUSTER are included in the default software installation but require a license from Global Phasing for activation. Copy your license file to /programs/local/buster/autoproc_licence or /programs/local/buster/buster_licence, respectively, and the software will start working. Academic members can register for a free license on the autoPROC and BUSTER websites.
BioXTAS RAW is now at version 0.99.9.14b. No additional information is available on this release.
CCP4 version 6.5.015 includes mostly updates and bug fixes with improvements to Refmac5, which now supports Mott-Bethe form factors for electron diffraction, and Pointless, which allows spacegroup without reindex.
DoGpicker was just added to the SBGrid collection. DoGpicker sorts particles by size using the radius of a particle.
EMAN2 was upgraded to version 2.11. With this version you'll see a bunch of bug fixes and performance improvements along with new support for the EMX data exchange format and CTFFIND parameter import, and initial support for displaying atoms in 3-D.
HKL2MAP is now at version 0.4. This update includes several minor bug fixes and a display of "real time" freely rotatable ribbon graphs for SHELXE auto-tracing models. Please note: HKL2MAP is not included in the default software installation. To include this software in your installation, please register here, then send a copy of your registration confirmation to us at firstname.lastname@example.org.
Modeller's upgrade to version 9.15 is primarily a bugfix release.
SCIPION is another application new to SBGrid. Scipion is an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.
UltraScan III version 3.3 is here! This new version contains enhancements for composite-jobs and Parallel Masters Groups that simplify MultiWavelength analysis. There are also changes that output a MonteCarlo model as a single multi-iteration record/file and fixes for handling of DMGA-RA-MC models.
xmipp version 3.2 was also pushed out. No release notes are available from the xmipp website.
Please don't forget to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.