Dear Consortium Members and Affiliates,
It's time for another SBGrid update, with news of our latest webinars, a profile on SBGrid member Daniel Minor, a couple critical operating system alerts, a software push with 4 updates and 2 new titles, 3 new members to welcome, a crystallography symposium in November, one new position posting, and 3 member publication highlights.
Many thanks to Tristan Croll for joining our monthly webinar and presenting on ISOLDE last week. You can find the recorded version of the webinar on the SBGrid YouTube channel. Make sure to join us on October 8th to hear from Nigel Moriarty on Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix. Webinar details here
What do frogs, powerlifting, and ion channels have in common? Daniel Minor from the University of California, San Francisco, who connected with us for our September SBGrid Tale and gave us some insight into the role frogs may play in developing a treatment to neutralize deadly neurotoxins. Read the full story.
We've got a couple of operating system alerts for those of you looking to buy new computers or update existing Mac or Linux machines:
• SBGrid is not compatible with MacOS 10.15 "Catalina", the next version of Apple's MacOS due out in October with significant changes. With Catalina, Apple will enforce strict filesystem controls that will break SBGrid installations. They have also dropped support for 32-bit binaries that many older applications require. We strongly recommend against upgrading to 10.15 on any Mac with SBGrid software. A solution is in the works, but it may take some time before we can fully implement the changes to officially support 10.15. We are also compiling a list of 32-bit software applications that will not be available after machines are updated to version 10.15.
• CentOS 8 support coming soon: CentOS 8 was released on 9/24 and we are testing SBGrid with plans to add support for this Linux distribution in the near future. We are not there yet, so hold off on those updates for now, but we expect the transition to be relatively smooth. With the addition of support for CentOS 8, we will move our build pipeline to CentOS 7 and begin phasing out support for new titles on CentOS 6.
Our September software push includes updates to CCP4, pandas, PyEM, and Python, and two new titles: CRISPRCasFinder and Slingshot. See Software Changes below for complete details.
Three new members joined SBGrid during September: Robert Dick from Cornell University, William DeGrado at University of California, San Francisco, and Ashley Spies of the University of Iowa. Welcome to our newest members!
Community Announcements / Position Postings
Crystallography in the 21st Century: November 8, 2019 at Columbia University -- NE-CAT and Cornell University are hosting a symposium dedicated to Dr. Kanagalaghatta (Raj) Rajashankar, with an fantastic group of speakers coming together to honor what Raj contributed to the community in his life and work. Details & registration here.
Senior Research Computing Scientist: The structural biology Advanced Research Computing (ARC) team at SBGrid / Harvard Medical School has a position opening for a Senior Research Computing Scientist. The ARC team designs, implements, and maintains a specialized computing infrastructure to support all phases of macromolecular structure determination via CryoEM, X-ray Crystallography, and NMR and works in close collaboration with SBGrid Consortium staff. Details & apply
Over 80 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple of notable highlights below:
• Vanderbilt University's Jens Meiler has a new paper in PLoS ONE that offers new insight into long QT syndrome type 1 (LQTS), an inherited disorder that causes cardiac arrhythmia. Since LOF mutations in the KCNQ1 potassium channel are responsible for type 1 LQTS, the authors work to generate structural models of KCNQ1 in the resting/closed and activated/open states in order to better understand the molecular basis for KCNQ1 LOF and to develop new therapeutics. Their study reinforces already available data that protein destabilization as a result of mutation is a frequent cause of KCNQ1 dysfunction. Abstract
• A new publication from Jason McLellan of the University of Texas at Austin, which appeared in Cell Reports this month, focuses on the Middle East respiratory syndrome coronavirus (MERS-CoV), which causes severe acute respiratory disease. In pursuit of vaccine development to combat this zoonotic pathogen, the researchers concentrated their study on G2, a neutralizing antibody that targets the MERS-CoV S1 N-terminal domain (S1-NTD), and discovered that G2 prevents the binding of MERS-CoV spike (S) protein to its receptor, DPP4. Abstract
• From our graduate student desk, Harvard student Kristen Rodrigues highlighted a publication from the laboratory of Daved Fremont that appeared in Cell Reports, in which the authors attempt to develop two Zika virus vaccines using a gorilla adenovirus vector. These vaccines where tested in mice and hold out some promise for use in humans. Read more
If you're currently preparing a manuscript, please remember you can publish your datasets in the SBGrid Data Bank along with your PDB record deposit and publication submission to preserve your primary experimental datasets. We also recommend the following boilerplate language in all publications that report results obtained with SBGrid supported software:
Structural biology applications used in this project were compiled and configured by SBGrid .
 A. Morin, B. Eisenbraun, J. Key, P. C. Sanschagrin, M. A. Timony, M. Ottaviano, and P. Sliz, “Collaboration gets the most out of software.,” Elife, vol. 2, p. e01456, Sep. 2013.
Link to article: https://elifesciences.org/articles/01456.
Our eLife paper received 8 new citations this month, in articles from Marc Kvansakul's La Trobe University laboratory in Viruses: Crystal Structure of African Swine Fever Virus A179L with the Autophagy Regulator Beclin; University of Toronto's Lynne Howell in the Journal of Biological Chemistry: Ega3 from the fungal pathogen Aspergillus fumigatus is an endo-α-1,4-galactosaminidase that disrupts microbial biofilms; Daniel Kahne's group at Harvard University in American Society for Microbiology: Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport; the laboratory of Ryan Hibbs at University of Texas Southwestern Medical Center in Neuron: Agonist Selectivity and Ion Permeation in the α3β4 Ganglionic Nicotinic Receptor; Jennifer Bridwell-Rabb's new publication in Biochemistry: Functional Annotation of ABHD14B, an Orphan Serine Hydrolase Enzyme; the Rockefeller University laboratory of Roderick MacKinnon in eLife: Regulation of Eag1 gating by its intracellular domains; from Jean-Philippe Julien at The Hospital for Sick Children Research/University of Toronto in Nature Communications: Potent antibody lineage against malaria transmission elicited by human vaccination with Pfs25; Samuel Butcher's group at the University of Wisconsin-Madison in Acta Crystallographica: Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking.
CCP4 is now at version 7.0.077, which includes an update to the xia2 interface in CCP4i, bug fixes in CRANK2, updates to refmac, crank2 and the deposition interface ccp4i2, a fix to the alternative conformer refinement in Coot, an SG search fix in mrbump, updates to the niggli cell and contaminants databases in simbad, and a fix to depositions in refmac5.
CRISPRCasFinder version 2.0.2 is new to SBGrid. CRISPRCasFinder enables the easy detection of CRISPRs and cas genes in user-submitted sequence data, an update of the CRISPRFinder program with improved specificity and insight into CRISPR orientation.
PyEM is now at version 0190718.
pandas 0.25.1 is the new default. We bumped pandas a few versions. See the website for detailed release notes.
Python version 184.108.40.206.4 was pushed out.
slingshot 1.3.2 was added to SBGrid. Slingshot is an R package that provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.
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.
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