Dear Consortium Members and Affiliates,
ONE. MORE. MONTH. And we can say goodbye to 2020 with hopes for a kinder, gentler 2021. Here at SBGrid we're just back from the Thanksgiving holiday to bring you the latest news: November webinar recordings posted to YouTube and our December lineup, a profile on SBGrid member James Hurley from UC Berkeley, one new software title and 13 updates, 5 new members to welcome, and a couple of member publication highlights.
November webinars included presentations from Vicky Higman on CcpNmr and, from the Icahn School of Medicine, Rinku Jain on Cryo-EM Structure & Dynamics of DNA Polymerase Delta in High-Fidelity DNA Synthesis and Radhika Malik on Cryo-EM Structures of DNA Polymerase Zeta in Translesion DNA Synthesis. You can catch up on all three on the SBGrid YouTube channel.
For our November member tale, we caught up with James Hurley from University of California, Berkeley whose days are devoted to protein-membrane interactions, ESCRT complexes, autophagy of mitochondria, a lot of cycling, and a dash poetry. Apropos of our times, Hurley made the leap to structural biology after learning that scientists were examining 1918 flu pandemic mutations to help explain bird flu in humans. Read the full story.
Our November software push includes one new title - nmrglue - and 13 updates: ATSAS, CCPEM, DIALS, DireX, HADDOCK, HKL2000, ImageMagick, IMOD, MotionCor2, python, RELION, Rosetta, and Schrodinger.
November brought us five new members, Fred Sigworth of Yale University School of Medicine, Ci Ji Lim and Katrina Forest at the University of Wisconsin-Madison, Stefano Ciurli at the University of Bologna, and Oluwatoyin Asojo of Hampton University, and Pumtiwitt McCarthy of Morgan State University. Welcome to our newest members!
Technical Updates from the Software Team
SBGrid does not support MacOS 11.0 “Big Sur." Big Sur is out, and it introduces BIG changes, with new compatibility for Apple Silicon ARM-based computers along with numerous other changes and security enhancements. We recommend waiting to upgrade any system required for scientific data processing. SBGrid officially supports MacOS 10.14 Mojave or 10.15 Catalina. Testing is underway to extend support to 11.0 Big Sur and we've added this page to our wiki to collect known issues: https://sbgrid.org/wiki/big-sur
Novartis has an opening for a Data Scientist: Are you a curious and inspired Data Scientist passionate about bringing protein science data to the next level of informing and impacting drug discovery projects? Do you like working in cross-functional and multidisciplinary teams? Do you enjoy transforming scientific challenges into computational solutions to catalyze efficiency in data-driven drug discovery? As a team member of a global Data Science group with expertise in protein data science, data engineering, computational biology, bioinformatics, screening analytics and predictive modelling this is a unique opportunity waiting for you to leverage protein science data at scale. See full posting
Over 50 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:
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:
SBGrid's eLife paper received five new citations in the month of November, from these SBGrid-member laboratories: Sanofi's Yanfeng Zhou in Journal of Biological Chemistry: A highly potent CD73 biparatopic antibody blocks organization of the enzyme active site through dual mechanisms and Antibodies: Bringing the Heavy Chain to Light: Creating a Symmetric, Bivalent IgG-Like Bispecific; Mark Kvansakul of La Trobe University in Biochemical Journal: Crystal structures of ORFV125 provide insight into ORF virus mediated inhibition of apoptosis; and Cristina Paulino at University of Groningen in Science Advances: Gating by ionic strength and safety check by cyclic-di-AMP in the ABC transporter OpuA.
ATSAS was bumped to version 3.0.3.
CCPEM version 1.5.0 includes a new cryoEF task for determination of completeness of particle orientations, a SIDESPLITTER executable and wrapper for use from RELION 3.1, EMDA programs and Python package for difference and average map calculations, Haruspex in alpha mode, a new option for generating maps from atomic models, AceDRG for generating ligand dictionary files, and B-factor analysis in Validation:Model task. Also, RELION was updated to version 3.1, Coot to version 0.9.2-pre, and LocScale now uses Gemmi for MTZ to MRC conversion.
DIALS was bumped to version 3.2.1
DireX 0.7.1-rev409 added a new turbo mode (command line argument -turbo) so that a new model map is not computed at each step.
HADDOCK 2.4 changes how input data are defined and uses run.param, a simple ASCII text file with a list of keywords and associated files.
HKL2000 721 includes a new default internal text editor, adds new program“rename_frames”, for use when the name template does not match the convention expected by HKL-2000/HKL-3000. adds supports the Bruker Photon III M28 detector format, the HyPix-6000HE modified format [785 x 813 pixels], and the PAD4M format using the new Oxford frame format, and MicroED can now process data collected with the Thermo Fisher Scientific CETA-D Micro ED detector.
ImageMagick version is 7.0.8-7 is available.
IMOD was updated to version 4.9.13 by default, and available by version override is the beta 4.10.51.
nmrglue 0.7 is new to sbgrid. nmrglue is a module for working with NMR data in Python. When used with the numpy, scipy, and matplotlib packages nmrglue provides a robust interpreted environment for processing, analyzing, and inspecting NMR data.
Python was updated to version 2.7.18.
RELION 3.1.1 supports the EER movie format for Falcon4, changes the defect correction to use a random pick from neighboring good pixels, instead of averaging them, fixes keep_ctfs_micrographs in Extract to respect the optics groups in the micrograph STAR file, updates Gentle Clean to delete temporary files from CtfRefine, and merges optimizations for GPU (--gpu) and Intel CPUs (--cpu) contributed by NVIDIA and Intel engineers.
Rosetta 3.12 is the new default, which includes the addition of constel0, for extracting constellations of atoms from a protein structure and restype_converter, a utility to convert between residue representations. Several new tools were also added including a ROSETTA_CRASH.log file on errors, new RelaxScripts, SliceResidueSelector, AcceptToBestMover, which replicates the accept_to_best command from inside FastRelax, and stepwise, a sampler and infrastructure for general polymers
Schrodinger 2020-4 is out. You can see the full list of updates in the release notes.