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Dear Consortium Members and Affiliates,
Helllooooo November! This time next week, with a little luck, election madness will be over here in the states (PLEASE!) and we'll only have the blossoming pandemic to distract us from tasks at hand. Despite those distractions, we've had a busy month of webinars, 9 software updates and 3 new titles added to the SBGrid collection, a few technical notes from our software team, and three member publication highlights. Read on for full details, and to everyone who can, please be sure to VOTE!
Our webinar series continued in October with software presentations on MovableType, Scipion, and TranSPHIRE, along with talks from Sophie Gobeil and Kartik Manne in the laboratory of Priyamvada Acharya at the Duke Human Vaccine Institute. You can find recordings of all of these talks on the SBGrid YouTube channel. |
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Our October software push includes updates to CCP4, ChimeraX, COOT, cryoDRGN, DIALS, IMOD, TOPAZ, TranSPHIRE, and XPLOR-NIH, along with three new titles: jq, KLTPicker, and MapQ.
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Technical notes from our Software Team |
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Goodbye CentOS 6. CentOS6 was released on July 7, 2011. Its nearly 10-year run comes to an end Nov 30th, when it will officially becomes "End of Life" and will no longer receive updates or security fixes. We have transitioned the SBGrid build platform to CentOS 7 and will no longer compile software on CentOS6. While this change does not mean that SBGrid software will suddenly stop working on CentOS6 or that updates will cease, users may find that new software versions won't run, and importantly, that we cannot fix them. We recommend migrating to CentOS 7 or CentOS 8, which are supported until 2024 and 2029, respectively.
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Member Publications |
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Over 90 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 publish 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's eLife paper received 3 new citations in the month of October, from these SBGrid-member laboratories: Wesley Sundquist at the University of Utah School of Medicine along with Owen Pornillos and Barbie Ganser-Pornillos at University of Virginia in Science: Reconstitution and visualization of HIV-1 capsid-dependent replication and integration in vitro; Jean-Philippe Julien from the University of Toronto in Nature Communications: Structural characterization of the ICOS/ICOS-L immune complex reveals high molecular mimicry by therapeutic antibodies; and Benjamin Spiller at Vanderbilt University Medical Center in PLOS Pathogens: The structure of the Type III secretion system export gate with CdsO, an ATPase lever arm;
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Software Changes |
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CCP4 is at version 7.1.006. The bump to 7.1 includes new versions of COOT, DIALS and DUI, the DIALS GUI, PHASER, SHELX, Buccaneer, ARP/wARP, and CCP4i2. New titles include GEMMI, MRparse, CCP4 Cloud, CCP4build, and a BUSTER interface,
ChimeraX is now at version 1.1.1 is available via version override. See what's new in the detailed change log.
COOT version 0.9.1 is out and has several new features, including fat atoms for some metals and halides, "Rescale" for the density fit validation graph, an API option for the label_closest_atoms_in_neighbour_residues and add_nucleotide(), an option to display the missing-residue loops set_draw_missing_residues_loops(), ability to find pep-flips using the based on difference map, new "Proportional editing" for atom-pull neighbor displacement, carbon atoms in Colour-by-Chain mode have their own color index, a a menu item for adding hydrogen atoms, an option to decolonize backup file names, an optio to reverse the hand of Cryo-EM maps using the flip_hand() function, and "Delete Residue" added.
cryoDRGN version 0.3.0b was pushed out. New in version 3.0: more visaulizations, updates to cryodrgn analyze,new features for particle selection and filtering in Jupiter notebooks, GPU parallelization with flag --multigpu, --amp flag for accelerated mixed precision training available for NVIDIA tensor core GPUs, and some tweaks to encoder and decoder arguments, and changes to these defaults: : --invert-data set to True, --window set to True, and kmeans volumes are now ordered according to distances in latent space.
DIALS 3.1.4 is now available. jq 1.6 was added to SBGrid. jq is a lightweight and flexible command-line JSON processor.
KLTPicker is also new 1.2.8. KLTpicker (Karhunen Loeve Transform) is a fully automatic EM particle picker that only requires an approximated particle size as an input and is designed to handle low SNR micrographs.
IMOD 4.10.49 is a beta version and is available via version override.
MapQ is yet another new tool in the SBGrid collection at version 1.5.4. MapQ assesses how well atomic model features are resolved in cryoEM maps by using a fitted model in the analysis and calculating a Q- for each atom in the model, then using Q-scores to visualize how well each residue/atom is resolved and averaged to represent the entire model/map.
TOPAZ version 0.2.5 has an updated user interface, adds Relion integration scripts and a Gaussian filter option for use after 3D denoising, and includes an update toTopaz extract that writes particle coordinates to one file per input micrograph.
XPLOR-NIH was bumped to version 3.1. See the changelog for details.
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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.
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More information about the SBGrid Consortium is available at http://sbgrid.org Report software bugs: sbgrid.org/bugs
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