Dear Consortium Members and Affiliates,
As we make the leap into spring we have the latest SBGrid update for you. Read on for some closing notes on our mini-symposium, a new Coot tutorial on YouTube, a reminder of next week's webinar on TomoAlign, a new SBGrid member tale, 12 software updates, two new members to welcome, and 3 member publication highlights.
Many thanks to the speakers and attendees who joined us last week for our mini-symposium on Low-Resolution Model Building in EM and X-ray Crystallography, hosted jointly with NE-CAT. We were thrilled to have attendees representing more than 40 different institutions for a dynamic and spirited discussion. A special thanks to NE-CAT's Cyndi Salbego and Frank Murphy for their help organizing behind the scenes, and a hearty congratulations to our three poster award winners: Morgan Abernathy from Pamela Bjorkman's Caltech laboratory, Moritz Hunkeler from the laboratory of Eric Fischer at Dana-Farber Cancer Institute, and Daniel Wrapp from Jason McLellan's laboratory at University of Texas, Austin.
We've added a webinar to our YouTube channel courtesy of Paul Emsley, who recorded a Coot Cryo-EM tutorial especially for our mini-symposium attendees. Up next: Cryo-Electron Tomography with José-Jesús Fernéndez joining us from the Spanish National Centre for Biotechnology. He'll give us a primer on TomoAlign for consideration of sample motion in cryoET. Join us next Tuesday, April 2 at 12pm EDT.
For our March member tale we got an introduction to the PARP family from John Pascal at the Université de Montréal, where he works alongside his wife, biochemist Marie-France Langelier. "We're PARP people," Pascal explains, and there are 17 members in this family of enzymes that have a hand in a wide range of biological pathways from antiviral response to organizing the mitotic spindle. Read the full story.
We pushed out 12 software updates in March, with new versions now available for AUTOPROC, BUSTER, CCP4, crYOLO, Dynamo, EMAN2, Fiji, MODELLER, Python, UltraScan III, VMD, and XDS.
March brought two new members to SBGrid: Jianwei Che from Dana-Farber Cancer Institute and Yong Xiong from the Yale University School of Medicine. Welcome to our newest members!
Member Publications
If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data in the SBGrid Data Bank along with the PDB record deposit and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
SBGrid's eLife paper received 3 new citations in member publications this month from Catherine Drennan of MIT in Nature Communications [Abstract]; Jacqueline Cherfils of Ecole normale supérieure Paris-Saclay in Nature Communications [Abstract]; and in a publication that appeared in bioRxiv jointly from the laboratories of Nikolaus Grigorieff and Leemor Joshua-Tor of HHMI Janelia Farm and Cold Spring Harbor Laboratories [Abstract].
Over 40 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple notable highlights below:
- In Current Opinion in Structural Biology is a new paper from Vanderbilt University's Tina Iverson, exploring the pathway of maturation of respiratory complex II with specific attention to intermediates formed during covalent flavinylation of the catalytic subunit, SDHA. [Abstract]
- Marc Kvansakul's team at La Trobe University in Australia published in FEBS Letters this month their study of the interactions between the human Scribble protein and Adenomatous polyposis coli (APC). Their investigation resulted in solving the crystal structure of the human Scribble PDZ1 domain bound to the PDZ-binding motif of APC. Since Scribble has been shown to have tumor suppressor properties, this structure could serve as a boon for cancer research.[Abstract]
- From our graduate student desk: Harvard student Kristen Rodrigues highlighted a publication from Harvard Medical School's own Stephen Harrison that appeared in Nature Scientific Reports. The authors asked why head-directed serum broadly neutralizing antibodies are more abundant than those that are stem-directed and compared autoreactivity profiles of these bnAbs types against human HEp-2 epithelial cells to gain a better understanding. [More on Tumblr]
Software Changes
AUTOPROC version 20190301 can now generate deposition-ready mmCIF files containing reflection data, a function that users can switch off by setting autoPROC_CreateCif=no. This version also has more robust handling of HDF5/Eiger dataset variants.
BUSTER version 20190301 will now compute DFc-completion map coefficients in the output MTZ file, with new columns in the refine.mtz file: 2FOFCWT_aniso-fill PH2FOFCWT_aniso-fill and 2FOFCWT_iso-fill PH2FOFCWT_iso-fill (more details in release notes). Also included is support for generating a deposition-ready reflection data mmCIF file containing final refinement data, added bond-typing to all relevant distributed restraint dictionaries, and initial support for electron diffraction (micro-ED).
CCP4 7.0.072 is available via version override. This version includes a new option to generate anomalous difference maps in dimple, a new dictionary accumulator in acedrg, improvements in CCP4i2 and CCP4i, and updates to simbad and panddas.
crYOLO version 1.3.0 includes a couple of new features: an interactive threshold selection after prediction; and an option to fine tune the general model for your data, making it feasible to do on a CPU and making training faster.
Dynamo is now at version 1.4.01.
EMAN2 the latest nightly build was pushed out and is available via version override.
Fiji was updated to version 20190218.
MODELLER was bumped a couple of versions to 9.21. This version has added support for Python 3.7, an update to the bundled version of HDF5 to 1.8.20, and updates to mmCIF models to contain metadata consistent with the draft MA mmCIF extension, describing the modeling procedure, custom restraints, templates used, and the alignment.
Python 3.7.0 update was pushed out. This latest version includes new C API for thread-local storage, core support for typing module and generic types, options to customize access to module attributes, along with many other performance improvements and bug fixes.
UltraScan 3 is now at version 4.0.2694.
VMD 1.9.4 was updated to the latest alpha (almost beta) release and is available via version override.
XDS version 20190315 includes an improvement so that when the user supplies a reading routine specified by the input parameter LIB=, expansion of the compressed images is now up to the external library routine.
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.