SBGrid Newsletter: February 2024

Dear Consortium Members and Affiliates,

Our February update includes webinar reminders, a software push with 11 updates and one new title, three new members to welcome, notes from the software team on operating systems to replace CentOS 7, and two publication highlights.

We are excited to have Prof. Sjors Scheres joining us from MRC Laboratory of Molecular Biology for our March software webinar to show off what's new in RELION-5.0. SBGrid's YouTube channel was also updated to include Björn Forsberg's January presentation on OccuPy. 

To receive email reminders about upcoming webinars, please be sure to register for the series! Registration here: https://sbgrid.org/webinars/#register

Mar 12: RELION-5.0 - Sjors Scheres

Apr 9: RFdiffusion - Brian Trippe

May 14: Free energy methods in Amber - Darrin York

Jun 11: TomoDRGN - Joseph Davis

July 9: matchmaps - Dennis Brookner

Webinar registration and details

SBGrid webinars are hosted with partial support from the NIH R25 Continuing Education for Structural Biology Mentors #GM151273, in collaboration with Co-PI Jamaine Davis of Meharry Medical College.

This month's software push includes updates to AlphaPulldown, aria2, autoPROC, BioXTAS RAW, BUSTER, Global Phasing Suite, IMP, OccuPy, POKY, Situs, and TexLive, along with one new title: Relion2Dynamo. See Software Changes below for complete details.

Three new members joined in February: the Dubochet Center for Imaging led by Alexander Myasnikov at École Polytechnique Fédérale de Lausanne, Gerhard Wagner from Harvard Medical School, and Kacie Ho of University of Hawaii at Manoa. Welcome to our newest members!

A few notes on operating systems as CentOS7 reaches End of Life. It’s time to move on, but with Red Hat’s changes to the CentOS model, where do we go? 

CentOS 7 End of Life

Ten years ago we announced support for software on CentOS 7 and we’ve been building and running software on that OS ever since. On June 30, 2024, CentOS 7 will reach End of Life and the last of the CentOS 7 security updates. 

Rocky Linux and Alma Linux fill the gap 

Alma and Rocky Linux can fill the gap left by the discontinued CentOS Linux stable release. Both are designed to be 100% binary compatible with Red Hat Enterprise Linux (RHEL). Like RHEL, they are focused on long-term stability for production-grade platforms. SBGrid is using Alma Linux internally on our workstations and we will support the nearly identical distributions of Rocky and Alma versions 8 and 9.

CentOS Stream takes the place of CentOS stable releases

CentOS Stream continuously tracks just ahead of Red Hat Enterprise Linux (RHEL) development and is midstream between Fedora Linux and RHEL. It serves as the upstream development branch of Red Hat Enterprise Linux. Note that CentOS Stream does not transition to “maintenance phase” after 5 years like RHEL-based distros. After development of CentOS 8 Stream ends on May 31, 2024 it will be archived and no updates will be provided. SBGrid software is supported on CentOS Stream and we expect it will be nearly identical to Alma and Rocky. With its shortened life relative to other distros (5 years), it makes more sense to choose Rocky or Alma, but SBGrid will work on this OS.

Ubuntu/Debian

We build and test software installations for RHEL-based distributions due to their long support lifetime and wide-spread use in High Performance computing facilities. While we don’t build or explicitly test software for Debian-based distributions like Ubuntu or Mint, we install software versions with required libraries and most software should work on these distributions. Users of these distributions should report issues when they find them and we will fix them if possible. 

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 Dierk Niessing from Helmholtz Zentrum München that appeared in Acta Crystallographica Section F describing a structure for the TRMT2A homolog in fruit flies, which can serve as a future target for Huntington's therapeutics. [Read more]

- Meharry Medical College student KeAndreya Morrison's highlight features a publication from the laboratory of SBGrid member Oriana Fisher of Lehigh University, in which the authors examine the role of a conserved amino acid residue in a family of bacterial copper-binding proteins. [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 two new citations since our last reporting, from these SBGrid members: 

Ryan Hibbs of University of California, San Diego in Cell: Structural mechanisms of a7 nicotinic receptor allosteric modulation and activation; Anthony Kossiakoff from The University of Chicago in Structure: Chaperone-assisted cryo-EM structure of P. aeruginosa PhuR reveals molecular basis for heme uptake

AlphaPulldown is now at release 1.0.4. The bump to 1.0 brought updates to Python and jax versions. There are now two singularity images, for the results generated prior to and after version 1.0.0. Users can also now integrate cross-link mass spec data with AlphaFold predictions via AlphaLink2 (see run_with_AlphaLink2.md), use multimeric templates for guiding AlphaFold predictions (see example_3.md), and have new options to compress or remove pickle files in the results directories to reduce the size of output directories.

aria2 version 1.36.0 is the new default.

autoPROC 20240123 is now available and includes support for the specification of extended module gap definitions to exclude sets of pixels and for calculating the absorption behavior as a function of energy of the sensor in CdTe detectors. A new macro ("-M SlippingCrystal") is available to improve processing of datasets where a significant change in crystal orientation makes the use of a single, overall orientation matrix inadequate and undermines the production of accurate integrated intensities, and a new tool ("aP_check_image_width") for detecting a discrepancy between the intended image width (as recorded in the metadata) and the actual width of the images collected during the experiment.

BioXTAS RAW is now at version. 2.2.2. The 2.0 update included several new features with the integration of CRYSOL into the GUI and API users can generate theoretical profiles by simply plotting a .pdb or .cif file, or open the CRYSOL analysis window and adjust the settings and fit the model to experimental data. A new profile comparison window provides residual and ratio plots, along with a heatmap of the probability profiles based on the selected similarity test. Users may also notice faster calculation of SVD and forward and backward EFA plots and an improved PDF report with text wrapping in columns. Be sure to check out the new publication describing BioXTAS RAW in the Journal of Applied Crystallography. 

BUSTER version 20240123 is out. This release includes a new command-line option "--eh99_sigma_correction" to address situations where the tighter sigma values produced by Grade2 are a concern, an update to Pipedream so that by default it will remove log-likelihood outliers as part of the series of BUSTER refinements performed, improvements to the 2D diagrams in Grade2 and the handling of metals and other single-atom residues in MakeLINK, and new tools: "fetch_PDB_gemmi" (replacing "fetch_PDB" script) for improved use of Gemmi for the conversion of
deposited PDB structures into model and reflection files, and two new command-line tools for computing R-values ("buster_rvalues") or maps ("buster_maponly") 

Global Phasing Suite version 20240123 is out and available to for-profit members with a license. This version incorporates the changes to autoPROC and BUSTER noted above.

IMP was bumped a few releases to 2.20.1. Major changes since our last update includes improvements to NumPy support, new support for Python 3.10, and performance improvements to the scoring function when used for Monte Carlo sampling.

OccuPy was updated to release 0.1.13. 

POKY was updated to 11/27/2023j and is available in SBGrid as version 20240131.

Relion2Dynamo was addded to the SBGrid collection at version 1.0.5 for Linux. Relion2Dynomao converts Relion 4.0 Star Files to a dynamo table for tomography.

Situs 3.2 is now available. The developers are celebrating the 25th anniversary of Situs with a series of updates to include new tomography related tools. Now available are three new filament tracing tools for tomography: Spaghetti Tracer (spatrac; for semi-ordered filament bundles), Struwwel Tracer (strwtrc; for random oriented filament networks), and elConDe (elconde; for constrained deconvolution of semi-ordered filaments). Also new is modified pdb2vol to support resolution lowering of experimental density maps (hybrid maps), and an update to the latest FFTW library.

TexLive was updated to version 2023.

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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