Dear Consortium Members and Affiliates,
As April comes to a close, we begin to look ahead to the end of the academic year, the winding down of our webinar series for the season and ramping up as we prepare for SBGrid renewals. Read on for details on some changes and add-on support options for July renewals, a link to April webinars along with our May lineup, three new members to welcome, three member publication highlights, six new SBGrid eLife paper citations (for a total of 488), and a software push with twelve updates (CCP4, CCPEM, Coot, CryoAssess, DIALS, IMOD, MODELLER, MolScript, MoRDa, NEGGIA, RELION, and Python) and one new title (Namdinator).
We are preparing for 2021 renewals and would like to announce a few changes, which mostly reflects increasing demand for software support around CryoEM, and higher costs for some of our bundled commercial software that only a small percentage of SBGrid laboratories consistently use. PIs should have received an email with an option to opt-in for access to:
Last month we had a round of science webinars, featuring Daniela Fera from Swarthmore, Steve Meisburger from Nozomi Ando's group at Cornell University, Dhirendra Simanshu of the NCI RAS Initiative at Frederick National Laboratory for Cancer Research, and Evris Gavathiotis of Albert Einstein College of Medicine. Jason Key also gave a little preview of our new SBGrid GUI-based software installation manager. You can find most of these talks on the SBGrid YouTube channel.
Our April software push includes updates to 12 titles: CCP4, CCPEM, Coot, CryoAssess, DIALS, IMOD, MODELLER, MolScript, MoRDa, NEGGIA, RELION, and Python. We also added one new title: Namdinator. Coot version 0.9.5 is now available, and according to the Coot Blog, was released "in the hope that someone will use it for the 2021 EM Validation Challenge." This version brings control of the weights to the user-level through the Refinement and Regularization Control widget. Torsion esds were also tightened for rotamer restraints. Coot’s cif parser also changed to use restraints that contain nuclear distances for hydrogen atoms preferentially.See Software Changes below for complete details.
Three new members joined the SBGrid community in April: Adrian Salic of Harvard Medical School, James Wachira of Morgan State University, and Michael Nilges from Institut Pasteur. Welcome to our newest members!
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:
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:
SBGrid citations: SBGrid's eLife paper received 6 new citations in April, in publications to which these SBGrid-member laboratories contributed: Sarah Bowman from the Hauptman–Woodward Medical Research Institute in IUCrJ: Structural biology in the time of COVID-19: perspectives on methods and milestones; Christopher Garcia from Stanford University in Immunity: The tissue protective functions of interleukin-22 can be decoupled from pro-inflammatory actions through structure-based design; Adam Frost from University of California, San Francisco in Nature Plants: Photocatalytic LPOR forms helical lattices that shape membranes for chlorophyll synthesis; Jonathan Abraham of Harvard Medical School in PNAS: Transferrin receptor targeting by de novo sheet extension; Shaun Rawson from Harvard Cryo-Electron Microscopy Center for Structural Biology in Nature Structural & Molecular Biology: Structures of chaperone-associated assembly intermediates reveal coordinated mechanisms of proteasome biogenesis; and Navtej Toor from University of California, San Diego in IUCrJ: Cryo-EM structure of a thermostable bacterial nanocompartment.
CCP4 7.1.013 includes an update to arcimboldo, coot, ccp4cloud, and mrbump and a fix to qtpisa command-line arguments.
CCPEM nightly builds were updated to versions 20210312 (Linux) and 20210224 (Mac). Nightly builds are available via version override.
Coot version 0.9.5 is now available, and according to the Coot Blog, was released "in the hope that someone will use it for the 2021 EM Validation Challenge." This version brings control of the weights to the user-level through the Refinement and Regularization Control widget. Torsion esds were also tightened for rotamer restraints. Coot’s cif parser also changed to use restraints that contain nuclear distances for hydrogen atoms preferentially.
CryoAssess 0.2.1 fixes a bug in the prediction results and creates a score file as the output for use in threshold selection.
DIALS 3.4.2 introduces a couple of fixes.
IMOD 4.11.4 fixes a number of bugs..
MODELLER 10.1 is a minor update that adds support for Apple Silicon.
MolScript 2.1.2-64b is a 64-bit recompilation available via version override for MacOS 10.14 and later. We received several support requests from users unable to use MolScript because the 32-bit version no longer works on newer MacOS.
Namdinator 20191016-5814c947 was added to SBGrid. Namdinator is a commandline tool, written in BASH, that sets up and runs a MDFF (molecular Dynamics Flexible Fit) simulation in a semi automatic manner, using only the input PDB file and input density file.
NEGGIA was updated to release 1.1.1.
Python 3.8 was pushed out.
RELION version 3.1.2 is now available. With this update, you'll find a new version of the wiki on RELION ReadTheDocs, a requirement for libtiff since it is necessary for compilation, an update to FFTW 3.3.8 and support for the AMD-optimized version, a bug fix in 3DCTF, support for TIFF images in CTFFIND, and support for SIDESPLITTER along with a several other fixes.
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 https://sbgrid.org
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