Dear Consortium Members and Affiliates,
It's the calm before the storm as the August holidays wind down and we prepare for the launch of the academic season. We've got an abbreviated version of our usual newsletter for you, with information on new ways to access data sets stored in the SBGrid Data Bank, a reminder that we will resume our webinar series in September, a small software update, a member lab position posting, 3 new members to welcome, and 3 member publication highlights. Best wishes to all during summer's last splash!
Accessing data sets stored in the SBGrid Data Bank just got easier. The PDBe has a new Experiment Data Component that allows users to link directly from PDB entries to the related primary data sets stored at the SBGrid Data Bank and similar repositories. Read the PDBe’s full press release -- Raw experimental data for 3D structures highlighted at PDBe -- and learn more about the SBGrid Data Bank.
Our webinar series will be back up and running in September, with a first presentation from Lance Westerhoff on Phenix/DivCon, a linear-scaling, semi-empirical quantum mechanics program (DivCon) combined with the Phenix X-ray refinement engine. See the current webinar lineup on our website.
We pushed out a small software update in August with updates to CCP4, CrystFEL, and Python, and one new application: Tomoalign.
Our member lab position postings page has been updated with a call for applications for a Senior Scientist in Cryo-Electron Microscopy position in Antonina Roll-Mecak's laboratory at the National Institute of Neurological Disorders and Stroke in Bethesda. Read more.
Three new members joined our ranks in August, hailing from two institutions also new to SBGrid: Liang Tang and Darcie Miller, from St. Jude Children's Research Hospital, and Ho-Leung Ng at Kansas State University. Welcome to our newest members!
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 was cited in two August publications. These 2 new citations came from the lab of Oliver Ernst at University of Toronto in an article that appeared in the Journal of Molecular Biology [Abstract], and a paper co-autnhored by Weikai Li from the Washington U & School of Medicine, St Louis that appeared in Biochimie [Abstract].
More than 20 member publications appeared in journals this month. You can find a complete listing on our website, along with a few notable highlights below:
- In Structure this month, Frank Sicheri of the University of Toronto examines a member of the NDR family of kinases, known to play a regulatory role in cell growth, by solving the structure of an inactive NDR1 kinase domain. His research reveals the auto-inhibitory role of the elongated activation segment of the NDR1 kinase and indiicates that regulation by MOB1 binding and by elongated activation segment act through separate channels. [Abstract]
- On the leukemia research front, Georgios Skiniotis of Stanford University has a new paper in Cell where he presents the cryo-EM structure of an active H3K4 methyltransferase COMPASS complex and delves into the relationship between the structural organization and conformational dynamics. [Abstract]
- From our undergraduate desk: Harvard student Kristen Rodrigues chose a PNAS publication from Christopher Garcia's group at Stanford University in which the authors describe how they engineered a peptide "velcro" to investigate the relationship between TCR/pMHC interaction affinity and cross-reactivity and report that peptide-dependent T cell activation was induced using the peptide velcro.[More on Tumblr].
CCP4 is now at version 7.0.061.
CrystFEL version 0.7.0 is now available. Key features include a new options system for indexamajig, removing most of the indexing method flags and adding functionality to automatically determine which indexing methods. Also new is the incorporation of the spectrum-based partiality model and numerical post-refinement algorithm from Ginn et al [Acta D71 2015 p1400] and new automatic tracking of the symmetry of the merged reflection list, eliminating the need to give the "-y" option to compare_hkl and check_hkl.
Python versions 2.7.15 & 3.6.5 were pushed out.
TomoAlign is new to SBGrid. The programs in TomoAlign are used for cryo-tomography tilt-series alignment and subsequent tomographic reconstruction that take into consideration beam-induced sample motion, modeled by means of polynomial surfaces.
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.