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Dear Consortium Members and Affiliates,
As June draws to a close and we all look ahead to a summer unlike any other and consider how we can seize this moment for positive change, we also continue in the usual vein with a new team member in another hemisphere, a story on SBGrid member Michael Cianfrocco, a new round of webinars to view online or join live, four new members to welcome, some technical notes from our software team, three member publication highlights, and a big software push with 18 updates and a couple of new tools.
In the wake of protests that continue around the country and beyond, as members of the Harvard community we are eager to amplify the calls for equality and social justice and build upon the momentum for change . We are involved in ongoing discussions around diversity and inclusion here at Harvard as part of the Better Together initiative, and will also examine what role we can play in broadening inclusivity in the structural biology community at large. Please contact Michelle Ottaviano if you would like to share any feedback or thoughts.
We are very pleased to introduce Pavel Filipčík, the newest member of the SBGrid team , who joins us through a collaboration with the laboratory of Kurt Krause at the University of Otago in New Zealand. Pavel will compile software and offer technical support, and help to fill a time-zone gap with a special emphasis on support for the Australasian community.
For our June SBGrid Tale , we spoke with Michael Cianfrocco from University of Michigan Life Sciences Institute about his recent work to develop a science gateway that could expand access to compute resources, and deep learning algorithms to automate the first step in the processing pipeline. Cianfrocco credits the recent advances in cryoEM for giving him more time to tinker. Whether tinkering at his computer or in the kitchen, his results will quench a thirst for something new. [ Read the full story ].
Our weekly webinars will continue throughout July per the schedule below, but we'll take a break in August. Be sure to let us know if you'd like to hear more about a particular software title or present on some recent science happening in your laboratory. June's lineup included a tutorial on RELION from Dari Kimanius along with presentations from Steve Reichow at Portland State University, Chris Hill at the University of Utah School of Medicine, Michael Robertson from Georgios Skiniotis's group at Stanford University, and Md. Mahfuzur Rahman from Ryan Hibbs's group, UT Southwestern, and just today, Evan Worden from Cynthia Wolberger's group at Johns Hopkins (we'll add this video so. Catch up on what you missed on the SBGrid YouTube channel .
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Our June software push includes updates to 18 titles: ARIA2, autoPROC, BioXTAS RAW, Bsoft, BUSTER, cryoDRGN, crYOLOd, DIALS, GPHL, GROMACS, LigPlot+, OpenMPI, Perl, Phenix, RELION, Sphire, Topaz, and XDS. We also added one new title - RADDOSE-3D - and a GPU accelerated version of ISAC to Sphire. See Software Changes below for complete details.
We had four n ew members join in June: Aneel Aggarwal from Icahn School of Medicine at Mt. Sinai, Mihnea Bostina from University of Otago in New Zealand, Anna Maciag from Frederick National Laboratory for Cancer Research, and new users from Seqirus. Welcome to our newest members!
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Technical notes from our Software Team |
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Update required for SBGrid Installation Client: last week we discovered that a certificate referenced by our client had expired resulting in a failure to connect to our servers and an erroneous "Missing Internet connection" error. This issue impacts version 1.0.694 and earlier for macOS and Linux and was corrected in the latest version, available here: https://sbgrid.org/wiki/client_downloads . Activated users can download the new version and use it without additional activation or registration steps.
Note to RELION 3.1-beta users: new versions require OpenMPI 3.1.6. You can find more information here https://sbgrid.org/software/titles/relion
July 24th outage possible : Harvard will relocate SBGrid's data center on Friday, July 24th, which may result in some downtime for SBGrid servers. We will notify technical contacts for your laboratories with additional information as it becomes available.
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Member Publications |
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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:
If you're currently preparing a manuscript, please remember you can p ublish your datasets in the SBGrid Data Bank along with your PDB record deposit and publication submission to preserve your primary experimental datasets. We also recommend the following boilerplate language in all publications that report results obtained with SBGrid supported software: |
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SBGrid member laboratories cited our eLife paper in six publications during the past month, including preprints in bioRxiv from Jean-Philippe Julien 's University of Toronto laboratory: Structural ordering of the Plasmodium berghei circumsporozoite protein repeats by inhibitory antibody 3D11 ; Ivan Campeotto from University of Leicester: Structure of the cysteine-rich domain of Plasmodium falciparum P113 identifies the location of the RH5 binding site ; and Dirk Slotboom 's contribution from the University of Groningen: Structural basis for stereospecific inhibition of ASCT2 from rational design ; a Nature article from the laboratory of Daniel Kahne at Harvard University: Structure of a nascent membrane protein as it folds on the BAM complex ; in Nature Communications a publication from Jennifer Bridwell-Rabb' s University of Michigan group: Structural basis for divergent C–H hydroxylation selectivity in two Rieske oxygenases ; and in from Cell Chemical Biology , a Sneak Peek from the MIT laboratory of Catherine Drennan : Molecular Basis of C–S Bond Cleavage in the Glycyl Radical Enzyme Isethionate Sulfite-Lyase
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Software Changes |
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ARIA version 2.3.2 is now compatible with CCPNmr Analsyis 2.4, produces new PDF reports, has improved Zinc ions patches, includes automatic superimposition of best structures and bundle RMSD, and introduces adaptive violation tolerance (cf Mareuil et al. J Bio NMR 015)
autoPROC is now at version 20200520 . This version improves handling of Eiger data (as mini-cbf files) at the indexing step, and the detection and optional exclusion of ice-rings. A new plot can also display the relation between spots found, spots in ice-rings, spots indexed, and multiple indexing solutions. Stabilizing measures were also introduced to avoid excessive shifts in the mosaicity/divergence parameters during integration, and in the error model parameters at the scaling stage.
BioXTAS RAW version 2.0.1 fixes a few bugs.
Bsoft is now at version 2.0.7.
BUSTER version 20200520 includes an update to buster-report to use the latest cctbx-based version of MolProbity and visualise-geometry-coot will now automatically load the MolProbity script when using the buster-report output directory. Pipedream now reports additional autoPROC and BUSTER statistics in both the summary.out and summary.xml files. The generation of TLS information in mmCIF files was improved and users can now use insertion codes in a residue range specification. aB_hydrogenate has a new fixing function, which runs on top of "hydrogenate" and ultimately Reduce, the aB_covalent_ligand tool, for use when generating restraint dictionaries for covalent modifications, allows users to use the Grade server if no local CCDC/CSD installation is available. Support was added for downloading CIF-only PDB entries with the "fetch_PDB" tool, new information about the hydrogen model used during refinement is included in the output PDB file, an error was fixed in handling ANISOU records in the "Boolean operation" tools aB_pdb_1and2, aB_pdb_1close2 and aB_pdb_1not2, and a fix was pushed to correct regression in the treatment of occupancies of hydrogen atoms.
cryoDRGN version 0.2.1 can parse RELION 3.1 files and fixes a compatibility issue with pytorch 1.5.
crYOLO version 1.7.2 is out. With the bump to 1.7 there is native support for maintaining the aspect ratio for K2/K3 images, filtering is now magnitudes faster on parallel filesystems, new "cleanup" and "skip" options allow users to delete filtered images after training/prediction is done and skip images that were already picked, a new experimental option normalizes with respect to the ice using Gaussian Mixture Model normalization, and the developers did a complete overhaul of documentation: https://cryolo.readthedocs.io
DIALS 3.0.1 drops support for Python 2.7. and includes a new best_monoclinic_beta parameter for dials.refine_bravais_settings and dials.symmetry to ensure that C2 is selected in preference to I2, and a new scaling model, model=dose_decay, implementing a shared exponential decay component for multicrystal experiments. The crystal model has a new recalculated_unit_cell attribute that allows storage of a post-refined unit cell in addition to that from traditional geometry refinement, and the dials.scale and dials.export commands will now use the recalculated unit cell where appropriate.
GPHL , the combined installation of autoPROC, BUSTER, and SHARP available to Global Phasing consortium members, was updated to the latest version.
LigPlot+ 2.2 is a major enhancement to the LIGPLOT program. New features include the an automatic superposition of related diagrams when two or more ligand-protein complexes are sufficiently similar, significant improvements to DIMPLOT, for plotting protein-protein or domain-domain interactions, a new links to view any LIGPLOT diagram in PyMOL or RasMol.
OpenMPI was updated to version 3.1.6.
Perl is now at version 5.30.1.
Phenix version 1.18.2 fixes weighting for iron sulfur clusters, introduces automatic creation of Amber files in the phenix.refine GUI and a new AmberPrep GUI, implements Engh & Huber restraints (2001) for cis-peptides, adds a new FeS restraint, sets the default metal coordination library to Zn+2 and FeS clusters, and adds a new global Ramachandran score for identifying protein structures with unlikely stereochemistry in CLI (phenix.rama_z, mmtbx.rama_z) and GUI (validation reports). Model-based density modification for cryoEM now has automatic model generation, in real-space refinement hydrogen atoms are no longer included in the map target function, which improves fit and the developers have added a NQH flip option. Users may also notice a new tool for ordered solvent picking in cryo-EM maps (phenix.douse), a map and model superposition tool (phenix.match_maps), a FindProgram option to find any Phenix program with a text search, and a new button in the .Project Details that opens a README file for tutorials.
RADDOSE-3D version 4 was added to SBGrid. RADDOSE-3D allows users to estimate the dose absorbed in a macromolecular crystallography diffraction experiment.
RELION 3.1-beta is now available via version override. This beta version includes high-order aberration correction in CTF refinement, an external jobtype to run third-party software in the RELION pipeline, schedules for designing & executing on-the-fly processing procedures, and tweaks to GUI, pipeliner, and helical processing.
Schrodinger is at version 2020-2.
Topaz version 0.2.4 was pushed out. This update adds 3d denoising and two pretrained 3D denoising models, and argument for setting number of threads to multithreaded commands, and improvements to the Topaz GUI.
XDS 20200417 corrects an error in the file headers of INTEGRATE.HKL, XDS_ASCII.HKL.
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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 http://sbgrid.org Report software bugs: sbgrid.org/bugs
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