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Dear Consortium Members and Affiliates,
Our February SBGrid update comes amid a disease outbreak that brings into focus the importance of science, health care workers, and public health. It brings with it renewed clarity from our side as we work to support structural biologists who are doing important work on this front and others.
To that end, we chug along with a call for beta testers for the latest version of our software installer, our monthly member tale featuring Alan Brown, a reminder about our March 10th webinar, a software push with 9 updates and 3 new titles, 4 new members to welcome, and 4 member publication highlights.
A call for beta testers. We're looking for a few good beta testers for new versions of our software installation client. Drop us a line at accounts@sbgrid.org if you'd like to get a jump on access to the latest updates, which will include multithreaded transfers, default-only version installation, automatic removal of obsolete titles, and better network diagnostics and troubleshooting. We'll have a GUI version available for testing soon as well.
Harvard Medical School's own Alan Brown is the focus of our March member tale. From race cars to cilia, movement and the engines that drive it are the fodder for much of his day. [Read the full story]
For our March 10th webinar, we're pleased to have Thorsten Wagner join us again, this time giving a primer on the automatic 2d class selection tool Cinderella. Webinar details here. If you missed last month's presentation on Schrödinger, you can watch that and other SBGrid-hosted webinars on the SBGrid YouTube channel.
This month's software push includes updates to autoPROC, BUSTER, CCP4, CrystFEL, DIALS, LigPlot+, Mono, MotionCor2, and TeX Live. We also added three new titles: CCMPred, ChemEx, and SIDESPLITTER.
February brought us four new members: Peter Walter from University of California, San Francisco and, from across the globe, Kurt Krause, Peter Mace, and Sigurd Wilbanks from the University of Otago in New Zealand. Welcome to our newest members!
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Member Publications |
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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: |
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SBGrid's eLife publication received 6 new citations during the last month, in articles from these SBGrid members and contributing developers: Ramachandran Murali of Cedars Sinai in a new Nature Medicine publication: iPSC modeling of young-onset Parkinson’s disease reveals a molecular signature of disease and novel therapeutic candidates; Tom Brett's Washington U School of Medicine, St. Louis group in Cell Reports: Structural and Biophysical Analysis of the CLCA1 VWA Domain Suggests Mode of TMEM16A Engagement; the laboratory of George Phillips at Rice University in BioRxiv: Prochlorococcus phage ferredoxin: structural characterization and interactions with cyanobacterial sulfite reductases; a Nature Chemical Cell Biology publication from Claire Metrick of Biogen: Human PLD structures enable drug design and characterization of isoenzyme selectivity; a recent Science article from the laboratory of Jason McLellan at The University of Texas at Austin: Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation; and from the developers of SPHIRE-crYOLO, an article in Communications Biology from Thorsten Wagner and Stefan Raunser of Max Planck Institute of Molecular Physiology: The evolution of SPHIRE-crYOLO particle picking and its application in automated cryo-EM processing workflows.
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Software Changes |
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autoPROC version 20200206 includes several new features: new iterative indexing options, anaspot - for analyzing SPOT.XDS files for ice-rings; an anaspot call will limit the found spots to the set resolution based on the current, idealised geometry, added high-resolution criteria with implementation of CC1/2 calculation according to Karplus & Diederichs (2012) paper, new analysis options with a new plot that combines divergence and mosaicity, the MTZANA tool for analyzing merged MTZ files, new command-line arguments -colcmpl and -nocolcmpl to print (or not) completeness per column.
BUSTER 20200206 includes improvements to restraint dictionaries (handling of torsion angle restraints for non-Grade dictionaries, access to CCP4 monomer library, improved heme dictionaries), occupancy refinement improvements in pdb2occ, a new macro for 2nd shell water addition, and TLS detection of empty or incorrect definitions.
CCMPred was added to SBGrid at version 0.3.2. CCMPred is software for protein residue-residue Contacts from Correlated Mutations PREDicted quickly and accurately.
ChemEx was added to SBGrid at version 2018.10.2. ChemEx is an analysis program for chemical exchange detected by NMR.
CrystalFEL was bumped to version 0.9.0. This update includes new options for wide bandwidth and electron diffraction processing, a new tool called cell_tool for operations on unit cell files, a new unit cell comparison algorithm, native handling of CBF files, and a change in ambigator so that resolution limits are no longer needed.
DIALS is now at version 2.1.2.
LigPlot+ was bumped to version 2.12.1.
Mono is now at version 6.8.0.96. See the Mono website for release notes.
MotionCor2 1.3.1 brings performance improvements along with fixes to the generation of the motion corrected stack, raw sum, and slow-loading of MRC movies.
SIDESPLITTER, a tool for mitigating local over-fitting during single particle reconstruction, is new to SBGrid. See more info on the SIDESPLITTER website.
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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.
This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium, the Structural Biology Grid computing consortium.
More information about the SBGrid Consortium is available at http://sbgrid.org Report software bugs: sbgrid.org/bugs
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