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Dear Consortium Members and Affiliates,
Spring is brimming with activity and with this month's SBGrid news we have a look at what's next in our current webinar series including details about our April 5th SBGrid workshop, some supplemental materials to share from our recent webinar speakers, a software push that includes 11 updates and 3 new titles, 12 new members to welcome, positions postings to share from SBGrid members at University of Leicester, and 3 member publication highlights. Read on! |
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Up next in the Spring Webinar Mini-Series: SBGrid Workshop: Register here for the SBGrid Workshop to learn more about the ins and outs of SBGrid, with team members Carol Herre, Pete Meyer, Shaun Rawson, and Jim Vincent presenting on Using the SBGrid Software Installer, AppCiter, and SBGrid Data Bank on PCs, HPC clusters and AWS cloud. Tuesday, April 5th from 11am-2pm EDT, learn more about: |
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The workshop is hosted by the U.S. National Committee for Crystallography (USNC/Cr). Register at https://www.nationalacademies.org/event/04-05-2022/sbgrid-consortium
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We were pleased to have a reprise of the popular sample prep and CryoEM computing webinars that we hosted last fall. Thanks to all of the speakers for joining us once again and for sending along the following supplemental materials:
Our March software push includes updates to 11 titles - Adxv, ATSAS, AutoDock Vina, Coot, DIALS, IMOD, iMosflm, PEET, ProDy, py4xs, and XDS - XDalong with 3 new titles: AlphaPickle, DUI, and Foldseek. See Software Changes below for complete details.
We had a BUSY March, with 12 new members joining us from 9 different institutions: Alaji Bah from SUNY Upstate Medical University, Bruce Beutler from University of Texas Southwestern Medical Center, Fasséli Coulibaly of Monash University in Australia, Shawn Douglas from University of California, San Francisco, Guillaume Dumenil from Institut Pasteur in Paris, Dmitry Lyumkis from Salk Institute, Eric Ortlund from Emory University, Greg Snyder from University of Maryland School of Medicine, Ronnie Berntsson, Erik Johansson, and Hussein Haggag/Centre for Electron Microscopy from Umeå University in Sweden, and Moderna. Welcome to our newest members!
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Community Announcements |
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Position Postings - University of Leicester University of Leicester has an opening for a Full-time, Permanent Lecturer position and two Postdoc positions available at the Department of Molecular and Cell Biology & Leister Institute for Structural and Chemical Biology, UK.
Full-time, Permanent Lecturer position: Application deadline: 25 April 2022
Postdoc positions: Application deadline: 11 April 2022 These positions are in the Panne group: The lab focuses on structural biology in the area of chromosome biology & gene regulation and infection & immunity research. For examples of recent work see Nature 578, 472–476 (2020); NSMB 27, 233–239 (2020); Nature 562, 538–544 (2018).
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Member Publications Highlights |
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Over 124 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:
Deposit your experimental datasets: If you're currently preparing a manuscript, please remember that, while you're making the PDB record deposit and publication submission, you can also preserve your primary experimental datasets with deposits to the SBGrid Data Bank.
Acknowledge SBGrid: SBGrid operations are funded with member fees and grants, so we are grateful when you are able to acknowledge SBGrid in your presentations and publications.
Please use this SBGrid logo on the acknowledgements slide of your presentations.
We recommend the following boilerplate language for inclusion in publications that report results obtained with SBGrid supported software: |
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Software Changes |
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Adxv 1.9.15 is the new default for Linux.
AlphaPickle 1.4.1 was added to the collection. AlphaPickle is a Python script for producing plots and user-legible files from the output of AlphaFold2 (notebook) and Colabfold (notebook).
ATSAS was updated to 3.0.5.
AutoDock Vina was bumped to 1.2.3. See recent updates in the changelog.
COOT 0.9.8 is the new Linux default.
DIALS 3.9.0 new features include: dials.background now writes to a log file, SHELX .hkl file output with dials.export, an output.clusters=True/False option to generate output for each clustersplit at a given threshold in dials.cluster_unit_cell, reindexing using multi-crystal reference data files in dials.reindex, the addition of CC½, plus a completeness column xia2.delta_cc_half , a new experimental dev.dials.ssx_integrate script for profile modelling and integration of SSX data, including ellipsoid profile modeling, an option to exclude_images= to take a single multi-sweep command for data reductions programs, a new flex.reflection_table.match_by_hkle method to match reflections between tables that have the same miller index and entering flags, and a new flex.reflection_table.concat method to concatenate reflection tables and handle experiment id remapping. There are also several new electron diffraction data processing options: PETS 2 exporting for processing electron diffraction data in dials.export, dials.find_spots, which calculates an average background in 2θ shells and identifies peak pixels above the background, and dials.powder_calibrate, a new tool to help calibrate the geometry of an electron powder pattern. (#2016)
DUI is another new title at version 2021.11.1. DUI is a DIALS graphical user interface, offering a new option for the general user to run DIALS tools and inspect the output.
Foldseek is new to SBGrid at version 1.3c64211. Foldseek enables fast and sensitive comparisons of large structure sets.
IMOD 4.12.18 beta is available via version override and adds a new 3D CTF correction.
iMosflm 7.4.0 has improved integration of very weak images. New features include: an option to display the phi profile of individual reflections, a tutorial covering processing of electron diffraction (MicroED) images (section 22), default values automatically set for the detector gain, polarization, dispersion, and beam divergence when processing MicroED images, improvements to the mosaicity estimation when dealing with data from very small unit cells, automatic recognition of images from beamlines at Petra (P14), Max IV and ESRF ID23 that have a vertical rotation axis, improved processing of Eiger detector header information, CBF images from the Bruker Photon II or Photon III detectors, and "pck" images from the Oxford Diffraction Crysalis detector, and better treatment of reflections where only a small number of pixels have a value less than or equal to the NULLPIX value.
PEET 1.15.1 adds coordinate import / export from Relion 4 STA (fromRunDataStar and to RelionCoords) and adds randomlySplit. ProDy was bumped several releases to 2.0.2.
py4xs is now at version 2022.1.5.0.
XDS 20220110 includes improvements for the Apple M1 processor.
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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 https://sbgrid.org Report software bugs: sbgrid.org/bugs
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