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Dear Consortium Members and Affiliates,
We're sending along our April update before we head into the weekend, with a reminder about the next webinar in our series on May 9th, a software push with 15 updates and 2 new titles, 9 new members to welcome, a final call from the RCSB Protein Data Bank to register for their upcoming Virtual Crash Course, a discount from Schrödinger for SBGrid members who would like to sign up for introductory courses, and three member publication highlights.
We have two webinars left in the series for this academic season. Join us May 9th to hear from Kevin Dalton of the Hekstra Laboratory at Harvard University on Careless, a tool that merges crystallography data, as the developers describe "without much physics." We'll have our April webinar on OpenFold posted to the SBGrid YouTube channel next week.
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Our April software push includes updates to AlphaFold, autoPROC, BCFtools, Bsoft, BUSTER, cryoDRGN, Geneious, Global Phasing Suite, GROMACS, ModelAngelo, OpenFold, PEET, R, TomoTwin-cryoet, PEET was bumped to release 1.17.0.and XDS, and two new titles: cryosparc-tools and DiffDock. See Software Changes below for complete details.
April was another busy month with new members joining, Andrea Dessen, Hugues Nury, and Martin Weik of IBS Grenoble, Joe Marcotrigiano of the National Institutes of Health, Emily Scott at University of Michigan, Gregory Melikian and the Electron Microscopy Core at Emory University School of Medicine, and new users at Takeda and Exelixis. Welcome to our newest members!
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Community Announcements |
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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 2 new citations in the month of April, from these SBGrid-member laboratories:
Jeremy Nathans of Johns Hopkins University School of Medicine in PNAS: Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae; Niraj Tolia from the National Institutes of Health in Nature Communications Biology: Structure of anhydrotetracycline-bound Tet(X6) reveals the mechanism for inhibition of type 1 tetracycline destructases.
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Software Changes |
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AlphaFold 2.3.2 has more robust downloads in Colab with shutil, an option to only run relax for the best unrelaxed model in the run_alphafold.py, improved documentation for ranked outputs and installation of aria2c, jax dependency removed from results pkl, Tensorflow update to 2.11.0, logic for _chem_comp.type is now case-insensitive for mmCIF parsing, along with a number of other performance improvements.
autoPROC 20230217 has a number of fixes and also now tracks ESDs associated with each refined cell parameter to allow writing of full-featured (extended) unmerged reflection data in PDBx/mmCIF format, has added support for Rigaku HyPix-Arc 150 datasets in cbf format, has a new parameter - AutoProcScaleMaxAllowedGapSize - which defaults to 99999 when automatic rejection is active (by default) or 5 otherwise, to allow users more control.
BCFtools version 1.17 is now available.
Bsoft version 2.1.3 is out.
BUSTER 20230217 changes include the use of loop constructs for nearly all categories in mmCIF restraint dictionaries produced by Grade2 in order to improve interoperability with external software, consolidated handling of ambiguous chiral centres in Grade2, a fix that makes sequences of BUSTER refinements within aB_autorefine behave correctly for the transfer of overall scaling B-factors across individual BUSTER jobs. Users may also notice additional control over occupancy refinement in the pdb2occ tool, and an option to allow NQH flips during model hydrogenation. The developers note that Grade is no longer supported and recommend using Grade2 for restraint generation.
cryoDRGN 2.2.0 includes new ab initio reconstruction tools (cryodrgn abinit_homo and cryodrgn abinit_het), a new utility script for writing cryoSPARC .cs files (cryodrgn_utils write_cs), improved plotting in cryodrgn analyze, and many codebase improvements.
cryosparc-tools 4.2.0 is new to SBGrid. cryosparc-tools is an open-source Python library that enables scripting access to the CryoSPARC cryo-EM software package.
DiffDock is another new tool at version 73ef67f. DiffDock is a state-of-the-art method for molecular docking.
Geneious 2023.1 major features include a new option to import DNAStar Lasergene SeqBuilder(Pro) .sbd file format, and Dotmatics Platform Integration Plugin that adds ability to register sequences in Bioregister. Geneious is available as an add-on option for all non-profit SBGrid members.
Global Phasing Suite, the combined installation of autoPROC, BUSTER, and SHARP available to Global Phasing consortium members, is now at version 20230222.
GROMACS release 2022.4 is now available.
ModelAngelo 0.2.4 is the new default.
OpenFold 1.0.1 includes new FP16 training, more stable training generally, and many fixes and performance improvements.
PEET was bumped to release 1.17.0.
R 4.2.3 (Shortstop Beagle) is now available.
TomoTwin-cryoet 0.3.0 is the new default. This update scales heatmaps to the same size as the tomogram, to allow easy overlay, and adds a command to make them optional, (–write_heatmaps). Also new: writing of Relion 3 STAR files required for WARP, and a change to make Reference refinement deactivated by default.
XDS 20220110_arm is available via version override to fix a problem with intel builds and neggia on M1. See our wiki page on overriding software versions: https://sbgrid.org//wiki/examples/versions
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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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