Newsletter

Dear Consortium Members and Affiliates,

Fall is off to a bustling start here at SBGrid, as we kicked off our webinar series mid-month, published a profile on SBGrid member Cynthia Wolberger, pushed out 12 software updates and 2 new titles, welcomed 5 new members, and have 3 software publication highlights from SBGrid member labs.

Our weekly webinar series got off to a good start in September with presentations from Prof Daniel Minor at UCSF, Daniel Wrapp, a graduate student in Jason McLellan's laboratory, and Prof. Qing Fan of Columbia University. All three are available on SBGrid's YouTube channel.

For this month's SBGrid Tale, we connected with Cynthia Wolberger at Johns Hopkins University School of Medicine, who credits her brothers' science books with sparking her interest in science. In the laboratory, Wolberger examines ubiquitin, chromatin dynamics and enzyme activity, but gets her greatest reward from acting as a mentor and her continued engagement with those who have passed through her lab, perhaps a little like the satisfaction she once got from a wink. [Read the full story].

Our September software push includes updates to autoPROC,  AWS CLI,  BUSTER, Global Phasing Suite, DIALS, emClarity, ImageMagick, Jalview, SHARP/autoSHARP, SPHIRE, NMRFAM-sparky, and SIMPLE, and the addition of two new titles:  deepEMhancer and TranSPHIRE. See Software Changes below for complete details.

Five new members joined in the month of September, with two from institutions that are new to SBGrid -  Eric Lee at the University of Ottawa in Canada and Shaun Stauffer at the Cleveland Clinic Lerner Research Institute - along with Michael Rout of Rockefeller University, Frank van Kuppeveld at Utrecht University in The Netherlands, and Ihn Sik Seong from Massachusetts General Hospital. Welcome to our newest members!

Technical notes from our Software Team

A quick reminder - as of Nov 30 2020 CentOS 6 will no longer receive maintenance updates and will no longer be supported. We recommend migrating to CentOS 7 or 8. A subset of SBGrid software will continue to work on CentOS 6, but users may be required to use older versions and may not be able to run new titles.

Member Publications

Over 100 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 4 new citations in the month of September, from these SBGrid-member laboratories:  Evripidis Gavathiotis of Albert Einstein College of Medicine in Nature: Inhibitors of BRAF dimers using an allosteric site;  Melanie Ohi of University of Michigan and Borden Lacy of Vanderbilt University have a new paper in eLife: Cryo-EM reveals species-specific components within the Helicobacter pylori Cag type IV secretion system core complex;  Ryan Hibbs from University of Texas Southwestern Medical Center with a new paper in Nature: Shared structural mechanisms of general anaesthetics and benzodiazepinesBrandt Eichman of Vanderbilt University in Journal of Biological Chemistry: An autoinhibitory role for the GRF zinc finger domain of DNA glycosylase NEIL3; and Ryan Hibbs of University of Texas Southwestern Medical Center in Nature:

Shared structural mechanisms of general anaesthetics and benzodiazepines.

Software Changes

autoPROC is now at version 20200918. See the release notes for full details.

AWS CLI version 2.0.24 is the new default.

BUSTER version 20200918  includes  aB_deposition_combine, a new tool to help create a single, deposition-ready mmCIF file from data-processing and refinement, along with many other fixes and improvements

Global Phasing Suite version 20200918 is available. This combined installation of autoPROC, BUSTER, and SHARP is available to Global Phasing consortium members.

deepEMhancer was added to SBGrid. deepEMhancer is a python package for non-linear post-processing of cryo-EM maps that performs sharpening-like and masking-like operations in a single step.

DIALS is now at version 3.1.2. This version includes several performance improvements, including for MPI for large datasets, a new max_images= parameter to limit the number of processed images, and a fix to the error when using split logs in dials.stills_process.
 

emClarity version 1.5.0 was pushed out.

ImageMagick is now  at version 20200918.

Jalview is at  version 2.11.1.0. With the bump to 2.11 there are some major changes, including support for loading VCF files and new filters and shading models for sequence features.

SHARP/autoSHARP version 20200918 was pushed out.

SPHIRE was updated to include GPU ISAC v 2.3. The Linux version of EMAN2 was updated to include version 2.3 of GPU-accelerated ISAC2. This program is available as sxisac2_gpu.py . Testing revealed significant differences in generated class averages to the previous version (1.2), and this version is still available as sxisac2_gpu.py.version1.2

NMRFAM-sparky was bumped to release 20200708

SIMPLE was bumped to version 3.03

TranSPHIRE version 1.5.0 is now available and is new to SBGrid. Transphire 

is a software package for fully automated processing of cryo-EM data sets during data acquisition This tool transfers data from the microscope, automatically applies common pre-processing steps, picks particles, performs 2D clustering, 3D refinement parallel to image recording, and introduces a machine learning-based feedback loop to re-train its internally used picking model to adapt to any given data set live during processing.

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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More information about the SBGrid Consortium is available at http://sbgrid.org

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