SBGrid Newsletter: September 2023

Dear Consortium Members and Affiliates,

News for September from the SBGrid team includes a member tale featuring Nozomi Ando of Columbia University, the launch of our new webinar series,  a software push with six updates and four new titles, seven new members to welcome, a technical note on MacOS Sonoma, and two member publication highlights.

Nozomi Ando is the focus of our September member tale. We caught up with her at Columbia University where her lab puts a high value on junk signals, or the often discarded  diffuse scattering signals that offer insight into proteins in motion. [Read more].

Join us on October 10th for the first software webinar of the season when we'll hear from Pablo Conesa on ScipionTomo. Mark your calendars and be sure to register for the series to receive connection details and reminders. [Register here].

Oct 10: ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation - Pablo Conesa
Nov 14: DiffDock - Gabriele Corso, Hannes Staerk, and Bowen Jing

Dec 12: DeepFoldRNA - Robin Pearce

Jan 9:

Feb 13: OccuPy  - Björn Forsberg
Mar 12:

Apr 9: RFdiffusion - Brian Trippe

May 14: Free energy methods in Amber - Darrin York

Jun 11: TomoDRGN - Joseph Davis

Webinar registration and details

This month's software push includes updates to AutoDock-Vina, crYOLO, HKL2000, TomoTwin-cryoet, MicroED-tools, and XDS, along with 4 new titles: CryoREAD, FPsim2, Infernal, and Napari. See Software Changes below for complete details.

Seven new members joined this month, including Thomas Grant and Devid Heppner from University at Buffalo, Constance Jeffery from University of Illinois Chicago, Kehinde Idowu from Texas Southern University, Hamidreza Sharifan of University of Texas El Paso, Leslie Vosshall from Rockefeller University, and Deborah Wuttke of University of Colorado, Boulder. Welcome to our newest members!

MacOS Sonoma: Version 14 MacOS Sonoma is out and we are actively testing and troubleshooting issues. If you decide to upgrade, please be aware that you may encounter issues we haven't found yet. If you do run into bugs, please let us know at bugs@sbgrid.org. 

Phenix GUI on MacOS14:  For those PHENIX users not on the mailing list, there are issues with the PHENIX GUI on MacOS 14. Command-line usage of PHENIX is less affected.

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:

- Fisk University student Vida Storm Robertson highlighted a publication from SBGrid member, Janet Smith of University of Michigan, who writes a wonderful academic and research history of recent Ewald Prize winner, Dr. Wayne Hendrickson, in the latest issue of International Union of Crystallography Journal.  [Read more]

- Meharry Medical College student KeAndreya Morrison's September highlight features a publication that appeared in PLOS One from SBGrid member Amy Andreotti of Iowa State University, which looks into specific interactions between Acalabrutinib and Tirabrutinib, two second-generation treatments for B cell malaginaces, and the target receptor BTK (Bruton’s Tyrosine Kinse) [Read more]

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.

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's eLife paper received five new citations since our last reporting, from these SBGrid members: Shaun Rawson of Harvard Medical School, in collaboration with researchers at Brigham and Women's Hospital, in Nature Structural & Molecular Biology: Structure of the preholoproteasome reveals late steps in proteasome core particle biogenesis; Niraj Tolia at the National Institutes of Health in Nature Communications:Structure-based design of a strain transcending AMA1-RON2L malaria vaccine; Jennifer Bridwell Rabb of University of Michigan in Journal of Biological Chemistry: The NADH recycling enzymes TsaC and TsaD regenerate reducing equivalents for Rieske oxygenase chemistry and in Nature Communications: Custom tuning of Rieske oxygenase reactivity; and Elizabeth Wright from University of Wisconsin-Madison in Nature Methods: Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex.

AutoDock-Vina 1.2.4 fixes a few bugs: details here.

crYOLO 1.9.4 fixes a bugs that caused crYOLO to freeze when predicting micrographs with certain naming schemes and that caused problems when writing cryosparc filament coordinates. Per a user request, crYOLO is writing filament start-end coordinates in star format again.

CryoREAD 2 is new to SBGrid. CryoREAD is a computational tool using deep learning to automatically build full DNA/RNA atomic structures from cryo-EM maps. 

FPsim2 0.4.5 is another new tool. FPSim2 is a small NumPy centric Python/C++ RDKit-based package to run fast compound similarity searches. 

HKL2000 is now at version 722.

Infernal is the third new title this month, at version 1.1.4. Infernal (INFERence of RNA ALignment) searches DNA sequence databases for RNA structure and sequence similarities using a special case of profile stochastic context-free grammars called covariance models (CMs). It is better capable, in many cases, of identifying RNA homologs that conserve their secondary structure more than their primary sequence. 

Napari python pkg0.4.18 is another new tool in the SBGrid Collection. Napari is a Python library for n-dimensional image visualization, annotation, and analysis. 

TomoTwin-cryoet 0.6 is 1.6x faster and linearly scales across multiple GPUs, 

exploiting the new compile option of the latest pytorch 2.1 nightly build and internally using DistributedDataParallel  instead of DataParallel.

MicroED-tools (formerly known as tvips-tools) was updated to 0.1.0-dev.7.

XDS 20230630 includes automatic removal of unused memory space in XSCALE, changes to XDSCONV and XSCALE to allow file names up to 256 characters, and avoidance of strange characters in standard output upon reading images using the DECTRIS neggia library.

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

Report software bugs: sbgrid.org/bugs