SBGrid Consortium - News and Events

Newsletter for April 2021

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Published April 2021

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:

•	A collection of 400 bioinformatics software titles via BioGrids.org, in a familiar SBGrid-style execution environment (Linux, OS X, cluster, and AWS installations are possible).
•	The Schrodinger Drug Discovery platform (license limited to labs in North America and Australia).
•	A pilot program to provide access to pre-configured CryoEM workstations, limited mostly to supporting smaller labs, available on a per project basis.
•	Geneious, a leading bioinformatics software platform.

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.

Upcoming SBGrid Weekly Webinars

May 4 - KLT Picker - Yoel Shkolnisky & Amitay Eldar, Tel Aviv University

May 11 - EMAN2 - Steven Ludtke, Baylor College of Medicine

May 18 - LightDock - Brian Jimenez-Garcia and Jorge Roel

May 25 - open - let us know if you would like to present

Webinar Details Here

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!

Member Publications

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:

•

In a Journal of Molecular Biology publication, Cristina Paulino of the University of Groningen, the Netherlands reviews recent advances in our understanding of the "groovy" TMEM16 protein family. Some groovy family members function as Ca2+-activated anion channels, while most are Ca2+-activated lipid scramblases, functional duality caused by small-ish rearrangements in the permeation pathway. [Abstract]

•

A new Microbiology Insights publication from Lynne Howell of the University of Toronto describes the bacterial biofilm matrix and a common denominator present in the matrix components of most Gram-negative bacteria, the Pel polysaccharide. The authors also discover a variant similar to Pel in many Gram-positive bacteria.

[Abstract]

•

From our graduate student desk, Harvard/MIT student Kristen Rodrigues highlighted a PNAS publication from SBGrid members Katherine Henzler-Wildman, University of Wisconsin–Madison, and Baron Chanda, now at University of Washington, St. Louis, and other researchers, that delves into the biophysics of temperature-dependent ion channel regulation using NMR spectroscopy and atomistic simulations to investigate the Shaker potassium channel in comparison to its engineered temperature-sensitive counterpart. [Read more].

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:

Structural biology applications used in this project were compiled and configured by SBGrid [1].

[1] A. Morin, B. Eisenbraun, J. Key, P. C. Sanschagrin, M. A. Timony, M. Ottaviano, and P. Sliz, “Collaboration gets the most out of software.,” Elife, vol. 2, p. e01456, Sep. 2013.

Link to article: https://elifesciences.org/articles/01456.

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.

Software Changes

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.

MoRDa 41 is the new default, which includes a new option to generate models of multimeric search models reduced to interacting domains, a new command line option to use a search model missing from the Morda database (using morda -f file_sf -s file_seq -p my_model.pdb
or morda_prep -f file_sf -s file_seq -p my_model.pdb). Users also now have a few more command line options for tweaking MR trials with a particular model, generated or provided by the user (Run morda_solve -h for details).

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.

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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