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Dear Consortium Members and Affiliates,
March seemed to come in like a lion and just keep on roaring. Here's a bit about what's been going on and what's up next from SBGrid: an April 11th OpenFold webinar, a software push with 14 updates and four new titles, seven new members to welcome, the retiring of two SBGrid computing portals, a new prerelease version of the SBGrid installation manager, new courses from community members (NE-CAT Practical Crystallography Course and RCSB Protein Data Bank Virtual Crash Course), Schrödinger course discounts for SBGrid members, and three member publication highlights.
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We have a big software push this month, with updates to CCP4, ColabFold, crYOLO, deepTools, DiffDock, EMAN2, FFmpeg, Fiji, GROMACS, IGV, ImageMagic, MotionCor2, PEET, and Schrodinger, in addition to four new titles: EMBuild, FreeSASA, OccuPy, and RELION Analyse Dashboard. See Software Changes below for complete details.
Seven new members joined SBGrid in March: Jan Pieter Abrahams from University of Basel, Daniel Hurdiss from University Utrecht, Alisha Jones from New York University, Chen Shen from Washington University in St. Louis, William Widger from University of Houston, Graeme Conn and Eric Sundberg from Emory University School of Medicine. Welcome to our newest members!
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Technical notes from our Software Team |
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Prerelease version of SBGrid installation manager. We are nearly ready to release version 2.9 of the SBGrid installation manager. This release includes a huge number of improvements and bug fixes. If you would like to try the latest prerelease version, see https://sbgrid.org/wiki/client_downloads#sbgrid-cli-prerelease-version.
Removal of obsolete RELION beta releases. We have removed many obsolete RELION beta releases from that SBGrid collection that are not supported by the developer and often contain known bugs. These older versions are available for reference if needed. If you have an older beta release configured in your ~/.sbgrid.conf file, you may see a “command not found” error. We recommend you use the latest 4.0.1 or 3.1.4 release. Retiring the SBGrid Science Portals. The SBGrid Science Portal launched in 2010 PMID 21098306. Since that time we have seen advances in cloud computing and HPC accessibility (ex OSG Connect), expanded access to computational resources, dramatic CPU performance improvements and increased adoption of GPGPU computation, improvements in crystallographic methods (CCP4Cloud PMID 36048148, SIMBAD PMID 29968670, MrBUMP PMID 29533225), and a revolution in the performance of ab-initio structure prediction and its utility for structural biology with the advent of tools like AlphaFold2 PMID 34265844, RosettaFold PMID 34282049, and CollabFold PMID 35637307. As such, after over 600 WSMR jobs, 500+ DEN jobs, and many millions of CPU hours, we are retiring the SBGrid Science Portals. We would like to thank the Open Science Grid for their support, both human and computational.
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Community Announcements |
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NE-CAT Practical Crystallography Course: June 21-23, 2023 at Harvard Medical School in Boston, MA. NE-CAT is pleased to offer a three-day Practical Crystallography Course. Hosted in conjunction with SBGrid, this course is free, but students are responsible for their own lodging and transportation. All students will need access to SBGrid during the workshop. More details
RCSB Protein Data Bank Virtual Crash Course: The RCSB Protein Data Bank will provide a course, "Use PDB data to their full extent: Understanding PDBx/mmCIF" on Wednesday, May 3rd 2023 from 1:00-3:00 EDT. Understand the basics of PDBx/mmCIF data dictionary and file format that underpin archiving of more than 200,000 experimentally determined three-dimensional biostructures in the PDB. Learn about software tools for generating and working with PDBx/mmCIF files, and programmatic access for harvesting PDB data. Program: https://iqb.rutgers.edu/sites/ Free registration: https://go.rutgers.edu/ Questions, please contact Michelle Sanghera: msanghera@iqb.rutgers.edu
Schrödinger Course Discounts: In partnership with Schrödinger, SBGrid members are entitled to a 25% discount on Schrödinger’s introductory online courses. See below for more information on the available courses:
To claim your 25% discount use the coupon code SBGrid25 when filling out the registration form for your course of interest. To access the registration pages you will need to have a Schrödinger web account - if you do not have one you may request one here. All requests should be processed in under 24 hours. If you have any questions about any of the courses or problems with your web account please email online-learning@schrodinger.com.
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Member Publications Highlights |
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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:
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: |
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SBGrid citations: SBGrid's eLife paper received four new citations in the month of March, from these SBGrid-member laboratories: Seth Darst of The Rockefeller University in PNAS: A general mechanism for transcription bubble nucleation in bacteria; Jason McLellan of The University of Texas at Austin in Journal of Bacteriology: Structural Basis for Binding of Neutralizing Antibodies to Clostridioides difficile Binary Toxin; Joseph Schlessinger of Yale University School of Medicine in PNAS: Cryo-EM analyses of KIT and oncogenic mutants reveal structural oncogenic plasticity and a target for therapeutic intervention; and Niraj Tolia at the National Institute of Health in Journal of Medicinal Chemistry: Structure-Based Design of Bisubstrate Tetracycline Destructase Inhibitors That Block Flavin Redox Cycling.
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Software Changes |
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CCP4 8.0.009 updates ccp4cloud to 1.7.010, ccp4i2 v2.0, pairef to 1.3, introduces fixes for refmac cif handling and pandda python3, updates ccif with mmcif_pdbx_v50.dic, and adds cbuccaneerNN, a new model building program and updates the monomers library with these new monomers: BJ3, BQG, CZU, DJ5, G5F, G7C, I1X, K39, P3C, UQO, WEL, WJB, ZN1, correction FES ColabFold 1.5.2 introduces a couple of fixes.
crYOLO 1.9.2 fixes a longstanding bug that caused Filament Mode to get stuck in certain cases.
deepTools is now at version 3.5.1.
DiffDock is new to SBGrid at version 73ef67f. DiffDock is a state-of-the-art method for molecular docking.
EMAN2 2.99 is the new default and includes a fully functional GUI for Deep Learning GMM dynamics/variability analysis (see this a mini-tutorial: https://youtu.be/1OM-XIzkSWw), a new subtomogram averaging refinement program that incorporates both 3-D subtilt and defocus refinement, a new single particle refinement program with modest resolution improvement over historical approach, HDF5 compression with bit reduction, and updated support for new EER variants, and other file I/O improvements.
EMBuild 1.0 is another new title. EMBuild is an automatic model building method of multi-chain protein complexes from intermediate-resolution cryo-EM maps that integrates AlphaFold structure prediction, FFT-based global fitting, domain-based semi-flexible refinement, and graph-based iterative assembling on the main-chain probability map predicted by a deep convolutional network.
FFmpeg 5.1.2 is now available.
Fiji 2.9.0 is the new default.
FreeSASA 2.1.2 is also new to SBGrid. FreeSASA is a command line tool, C-library and Python module for calculating solvent accessible surface areas (SASA). Casual users can calculate SASA directly from a PDB file with no configuration overhead using sensible default parameters. Advanced users can configure all calculation parameters and also use the C and Python APIs to perform calculations directly on arrays of coordinates.
GROMACS 2023 includes performance improvements, with and without GPUs, in addition to these new features: PME decomposition optimization to support offloading the entire PME calculation to multiple GPUs, including the FFT computation, new CUDA Graph support to execute GPU-resident single-/multi-GPU simulations using thread-MPI entirely, support for Apple M1/M2 GPUs via the OpenCL GPU backend, new ensemble temperature mdp options to set the temperature of the ensemble for simulations without temperature coupling or with different reference temperatures, native implementation of the DSSP algorithm with gmx dssp.
IGV 2.16.0 includes new color options for alignment tracks that display PacBio SMRT kinetics data (see more), a new option to apply grouping to all loaded alignment tracks, and feature to allow entry of multiple URLs separated by spaces in File > Load from URL.
ImageMagick version 7.1.1-3 is the new default.
MotionCor2 1.6.3 changes result in noticeable Thon ring improvement.
OccuPy 0.1.11 is new to SBGrid. OccuPy is a fast and simple python module and program to estimate local scaling of cryo-EM maps, to approximate relative occupancy and/or resolution, and equalize the map according to occupancy while suppressing solvent amplification.
PEET was updated to version 1.16.0a.
Schrodinger was updated to 2022-4.
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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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