SBGrid Consortium - News and Events

Newsletter for June 2021

Older
Newer

Published June 2021

DeOpening:

Dear Consortium Members and Affiliates,

A sigh of relief often accompanies the last days of June, with the flurry of fiscal year close and SBGrid renewal preparations mixing with a whirl graduations and recitals that all look a little different this year. Many thanks to all who are extending their Consortium membership for another year. Please be sure to read the notes from our technical team on accessing this year's add-on software options, watch our latest webinars, read a profile on scientist and software developer Stefan Raunser, welcome five new members, check out a few member publication highlights, and learn more about the 14 software updates that went out this month.

We hosted our final webinar of the season on Tuesday and were pleased to welcome Alexandre Bonvin to share the latest on HADDOCK, and earlier this month, Daniel Castaño Díez for an introduction to Dynamo. You'll find recordings for both of these presentations on the SBGrid YouTube channel. September's lineup will take shape soon, but please be sure to let us know if you'd like to learn more about a particular title or if there is new research from your lab you'd like to present.

For our June SBGrid Tale we connected with Stefan Raunser from Max Planck Institute of Molecular Physiology in Dortmund, Germany, a multi-instrumentalist now playing at structural biology in multiple modes, as a biologist examining threadworm bacteria with an eye to repurposing their toxin-delivering molecular syringes to deliver therapies, and leading a team of software developers creating tools for cryoEM and cryoET to dig deeper into the proteins and their spatial arrangement. [Read the full story].

This month's software push includes updates to these 14 titles: autoPROC, BUSTER, CCP4, CCPNMR, CryoAssess, DIALS, EMAN2, GPhL, Phenix, PyMOL, Relion Realtime Preview, Schrodinger, shelXle, and XDS. See Software Changes below for complete details.

We had five new members join in the month of June: Jeremy Baskin of Cornell, Tianmin Fu from Ohio State University, Aaron Smith at University of Maryland, Baltimore County, Jennifer Cash of UC Davis, and David Sibley from Washington University St Louis. Welcome to our newest members!

Technical notes from our Software Team

July 1 is the renewal date for our licensed software, so you may have noticed license expiration alerts for the following titles:

PyMOL: The license for incentive PyMOL available for non-profit users was renewed and updates were pushed out for site installations. If you are using the installation manager to install your software, be sure to kick off an update. If you think you have already updated the software and are still receiving a warning about an expired license, email us at bugs@sbgird.org.

Geneious and Schrodinger: Effective the July renewal, Geneious and Schrodinger* are only available to non-profit labs that have opted in and will pay an add-on fee. We have built in a 2-week grace period to ensure that all users have uninterrupted access and allow those who may have missed our earlier announcements to opt-in before access is disabled. We will update our Geneious and Schrodinger* license on July 1st, as in past years. In mid-July we will remove the licenses from general use and provide groups that have opted in with new configuration instructions. Contact us at accounts@sbgrid.org if you have questions.

*Schrodinger access is limited to labs in North America and Australia.

BioGrids is another á la carte option available to SBGrid members this year, which is an SBGrid-style collection of ~ 400 bioinformatics software titles developed with funding from Harvard Medical School and Boston Children's Hospital. For laboratories that have opted in for BioGrids, lab members can access this tool as follows:

•	If you are already using SBGrid's software installation manager to install SBGrid-supported software, you can use those same credentials to download the BioGrids installation manager. See the BioGrids wiki for instructions on how to download the BioGrids installation manager: https://www.biogrids.org/wiki/Home
•	If you are not yet using the SBGrid installation manager, this tool is a great option for individual users to install the software on workstations at home or in the lab. Register for the installation manager at www.sbgrid.org/registration/register/ and we can get you set up with instructions for using this tool to manage both the SBGrid and BioGrids software stacks.
•	For those who wish to add the full BioGrids software stack to their site installations, some groups may encounter storage issues. Please contact us at bugs@sbgrid.org to discuss the best options for installation.

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 Protein Science, Hazel Holden of the University of Wisconsin-Madison studies the L136 enzyme of Acanthamoeba polyphaga Mimivirus (APMV) to help elucidate the d-viosamine pathway of this giant virus whose structural and genetic complexity have attracted intense research interest. The authors present solved structures of L136 and examine its functional differences to another sugar aminotransferase, the structurally related DesI of the bacterium Streptomyces venezuela. [Abstract]

•

A new Cell publication from Carsten Sachse of Forschungszentrum Jülich in Germany unveils the cryo-EM structure of PspA of the phage shock protein system and discusses PspA's involvement in membrane remodeling, integrity, and function. [Abstract]

•

From our graduate student desk, Harvard student Kristen Rodrigues highlighted a publication that appeared in Science from the laboratory of Stephen Long at Memorial Sloan Kettering Cancer Center, which examines the structural basis of Hedgehog acyltransferase activity and demonstrates how HHAT allows substrates on opposite sides of the endoplasmic reticulum membrane to interact. [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 3 new citations in the month of June, from these SBGrid-member laboratories: Janosch Hennig from the European Molecular Biology Laboratory (EMBL) in Genes and Development: Divergent evolution toward sex chromosome-specific gene regulation in Drosophila; Jean-Philippe Julien at University of Toronto in Nature Communications: Multivalency transforms SARS-CoV-2 antibodies into ultrapotent neutralizers Acute pharmacological degradation of Helios destabilizes regulatory T cells; and Eric Fischer from Dana-Farber Cancer Institute in Nature Chemical Biology: Acute pharmacological degradation of Helios destabilizes regulatory T cells.

Software Changes

autoPROC version 20.04.2021 includes several new features: reporting of a so-called "operational resolution" to facilitate comparison of data processing results including anisotropy analysis by STARANISO, support in "imginfo" for CBF files, and support for detector serial numbers in mini-cbf files. You also may notice improved handling of HDF5 datasets, support for Mar345 (Mar Image Plate) formats, command-line checking for dataset specifications (-I, -Id and -h5 arguments), and a number of other updates.

BUSTER version 20.04.2021 includes "aB_I2_to_C2" and "aB_C2_to_I2", two new tools to move between C2 and I2 settings, a new Gnuplot binary that should improve timing on CentOS 8, improvements to the MTZ-checking step of a BUSTER ("refine") job, and handling multiple -RB flags and models with existing hydrogens when running aB_hydrogenate.

CCP4 nightly build 7.1.014 is available via version override.

CCPNMR 3.0.4 is a MacOS BigSur release with ARM compatibility. It includes general bug fixes for improved stability, graphical speed optimizations, improvements to Drag & Drop of NmrAtoms for ambiguous peak assignments, a new macro for calculating Distance Restraints from a PeakList (alpha-testing), support for small molecules, a bug fix for the NEF parser, improvements to ChemBuild with a fix to ChemComp (xml) export, new Pseudoatom support, GUI bug fixes, and a PythonConsole for direct macro-writing.

CryoAssess version 1.0 is available via version override. This version is not set as the default since there is a problem with 2DAssess. Version 1.0 includes big updates to MicAssess, which can now predict 6 labels with a goal of helping the user to identify the most promising micrographs (1-Great) and give information about why a micrograph is "bad" (labels 3-6). Labels include: 1-Great, 2-Decent, 3-Contamination, Aggregate, Crack, Breaking, Drifting, 4-Empty (no ice), 5-Crystalline ice, 6-Empty ice, no particles but vitreous ice. This version requires new model files, which consist of 4 different .h5 files. Since Relion 4.0 will have its own 2D classification auto-selection tool, the developers do not plan to update 2DAssess in the future.

DIALS 3.5.0 includes new bootstrap options: --mamba to install with micromamba, and --clean to remove installation caches immediately after completion, a new command - dials.find_bad_pixels - to identify pixels identified as signal in >= 50% of images, an option to allow processing of data too large to fit in memory in dials.integrate, in dials.scale an error_model.grouping= option to control refinement of error models during scaling and physical.absorption_level=[low|medium|high] for bulk control of absorption correction. You'll see significantly faster Rij matrix calculation of pairwise correlation coefficients in dials.cosym, a new selector to choose between the default "image" and traditional "lab" coordinate frames in dials.image_viewer, along with several other improvements.

EMAN2 20210616 nightly build for Mac and Linux is available via version override.

GPhL was updated to version 20.04.2021. Global Phasing Limited (GPhL) is available to for-profit industry members with a valid license.

Phenix 1.19.2-4158 is the new default and introduces a fix that caused the GUI to crash when running validation after phenix.real_space_refine along with other bug fixes.

PyMOL 2.5.0 includes several new features available only in the incentive version including multiple-level undo for PyMOL actions, improved MAE import, and an option extend nucleotides from the PDB in builder. Also new are curved cartoon cylindrical helices, customizable keyboard shortcut menu, and improved isosurface generation. Note that SBGrid does provide the incentive version.

Relion Realtime Preview version "gracefully" was updated to include the application Follow_Relion_gracefully, a simple python script which enables following the progress of Relion 2D/3D classification and refinement in a browser. It is available via version override.

Schrodinger 2021-2 is out. See details in the release notes.

shelXle version 1264 is now available.

XDS 20210515 was updated to support autoPROC.

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

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007