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Dear Consortium Members and Affiliates,
We begin this SBGrid update with the words that prefix every greeting in our new reality: we hope everyone is safe and healthy. We know this global pandemic challenges everyone in many different ways. Labs are closed, projects are shelved or reimagined, and many are forced to make difficult decisions about cell lines, animal models, and staff. As SBGrid strives to create support resources during this transition, we ask: how has the coronavirus pandemic impacted your research? Are you seizing the call to shelter-at-home as an opportunity to write a manuscript or master new software? Have you taken up a COVID-19 project?
Please tell us what is happening in your lab, how we can help, and whether you are interested in connecting with Consortium members to share experiences and advice. We'll explore ways to foster communication between the 350+ structural biology groups that comprise our Consortium, and for those who are interested, Carol Morton, our contributing science writer, can incorporate your experiences into a blog. Reply here to answer a few quick questions and share your story.
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In other SBGrid News: Thorsten Wagner from MPI Dortmund joined us for our March webinar earlier this month, to show us around his 2d class selection tool Cinderella. You can watch his presentation on the SBGrid YouTube channel. We heard from Tom Terwilliger today and will soon have his webinar posted. Up next: another Phenix webinar with Pavel Afonine on Friday at 12pm ET. See the Resources for Remote Work section below for more information on how we've re-tooled our monthly webinar series.
The focus of our March SBGrid Member Tale is Carsten Sachse, who directs the Ernst-Ruska-Centre 3 for Structural Biology at Forschungszentrum Jülich in Germany. Sachse credits the discipline and teamwork of childhood extracurricular sports for helping to prepare him for science, where he now straddles the worlds of wet lab biology and methods/software development, investigating the machinery of autophagy while creating tools for helical reconstruction (SPRING) and cryo-EM density maps (LocScale). [Read the full story].
March's software push includes updates to autoPROC, BioXTAS RAW, BUSTER, GPHL, Fasta, PEET, Schrödinger, and XDS, as well as one new title ShelXle. See Software Changes below for complete details.
Four new members joined in the month of March: Danica Fujimori and Ronald Vale from University of California, San Francisco, Ivelin Georgiev at the Vanderbilt University Medical Center, and Jianbin Ruan from University of Connecticut Health Center. Welcome to our newest members!
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Resources for Remote Work |
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Installation Client - use this tool to quickly and easily install SBGrid-supported applications on your workstations at home. Users can choose a graphical installer for Mac or command-line installer for Linux or Mac to pick-and-choose a subset of applications, install the full collection, and kick off updates when convenient. Register for the installer.
Weekly Webinar Series - every Tuesday and Friday at 12pm ET, join us to hear from developers and PIs on what's new in structural biology. Our May Symposium is being recreated in these twice-weekly webinars, with a hope to provide an opportunity for community members to connect and learn together. See the full webinar lineup.
Tips for getting the most out of SBGrid - new recordings from SBGrid team members James Vincent on using the SBGrid Installation Client for Mac GUI or Mac/Linux CLI and Pete Meter on remote work and structural biology computing, are available. We'll be adding some additional tutorials in the coming weeks, including an introduction to the newest beta version of our installer client from Jason Key and primer on SBGrid's capsule environment from Carol Herre. Check the SBGrid YouTube channel for these and our full collection of past webinars. |
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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Software Changes |
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autoPROC version 20200319 adds several new features. You'll notice a new option to generate PDF reports from scaling-only runs (using aP_scale), a new tool (aP_select_pdb) to help match newly processed data (MTZ file) to a sensible starting model, a new tool (aP_fixcbf) that tries to fix mini-CBF files containing erroneously masked pixels, and many other improvements and fixes.
BioXTAS RAW version 1.6.4 has a new header type for the MacCHESS SAXS beamline Eiger 4M detector along with some minor bug fixes.
BUSTER 20200319 includes a new feature to stabilize the refinement when TLS is involved using the TLSfreeze parameter, which switches off concurrent refinement of certain classes of variables in the big cycles that refine TLS parameters.
GPHL -- Global Phasing for industry members -- was updated to version 20200319.
Fasta was bumped a couple of versions now to 36.3.8h. Check the release notes for full details.
PEET version 1.14.0 is the new default.
Schrödinger was bumped to version 2020-1 v2.
XDS is at version 20200131, which includes revisions to the routine for collecting results from processing batches of images during the INTEGRATE step with a new input parameter - MAXIMUM_IMAGE_GAP_FOR_ADDING_PARTIALS= - that controls the addition of partial intensity contributions to the same reflection from adjacent image batches.
ShelXle is new to SBGrid at version 1.0.1070. ShelXle is a "cute" graphical interface for ShelxL
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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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