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Dear Consortium Members and Affiliates,
Spring is tantalizingly near, even as we shovel out from the latest storm, so we'll hunker down a little longer as we send along this monthly news: details about our March ModelAngelo webinar, a profile on SBGrid software contributor Andrea Thorn, a software push with nine software updates and one new title, two new members to welcome, and three member publication highlights.
Up next in our Software Webinar Series, join us on March 14th at 12pm EST when Kiarash Jamali will introduce us to ModelAngelo: Automated atomic model building for cryo-EM, the latest from the laboratory of Sjors Scheres at MRC Laboratory of Molecular Biology. If you missed Martin Steinegger's presentation on Foldseek earlier this month, keep an eye on the SBGrid YouTube channel. We'll have that one posted soon.
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This month's SBGrid Tale features Andrea Thorn, Group Leader at University of Hamburg, who has a passion for collaboration and second takes, whether recreationally as a role-play enthusiast, or in science where she became a public champion of both as the head of the Coronavirus Structural Task Force. [Read the full story].
Our February software push includes nine updates to AlphaPickle, BEDtools, Careless, CryoDRGN, crYOLO IMOD, NEdit, Python, and SAMtools, along with one new software title: DeepFoldRNA. See Software Changes below for complete details.
February brought us two new members: Elizabeth Draganova from Emory University and Vincent Nzuwah-Nziko from Hampton University. Welcome to our newest members!
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Member Publications Highlights |
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Over 50 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 during the last month from these SBGrid-member laboratories:
Jennifer Bridwell-Rabb from University of Michigan in Journal of Biological Chemistry: A structure-function analysis of chlorophyllase reveals a mechanism for activity regulation dependent on disulfide bonds; and Jean-Philippe Julien from University of Toronto in Immunity: Potent transmission-blocking monoclonal antibodies from naturally exposed individuals target a conserved epitope on Plasmodium falciparum Pfs230;
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Software Changes |
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AlphaPickle 1.5.3 fixes a bug in the handling of new format of PAE json files.
BEDtools 2.30.0 includes several new options: -ignoreD in the genomecov, which allows D CIGAR operations to be ignored when calculating coverage, -rna in getfasta to allow support for RNA genomes, to read reference genomes as an environment variable (CRAM_REFERENCE) when using CRAM input files. You also might notice performance improvements for parsing input files and printing results and several bug fixes.
Careless 0.2.7 includes a new --overall flag in ccpred, which pools results from multiple predictions files, and an update to skip normalization for metadata columns with zero variance.
CryoDRGN 2.0 is a beta version available via version override that includes new ab initio reconstruction tools: cryodrgn abinit_homo and cryodrgn abinit_het
crYOLO 1.9.1 is out with a new boxmanager based on napari with commands cryolo_boxmanager_tools.py createAutopick to create the necessary autopick.star for extraction in relion 4 and cryolo_boxmanager_tools.py class2Dextract to extract the coordinates of good 2D classes from RELION. Also new: a cryoSPARC output format that makes importing particles/filaments easier, RELION filament star files with precalculated priors, a validity check for lowpass filtered images, and miscellaneous small fixes.
DeepFoldRNA is new to SBGrid at version 20220912. DeepFoldRNA s a deep-learning based method for de novo RNA tertiary structure prediction from Yang Zhang's laboratory at University of Michigan Medical School.
IMOD 4.12.35 is a beta version with bug fixes available via version override.
NEdit 5.7-arm is available via version overide for compatibility with new m1 CPUs.
Python 3.9.16 is a bug fix release for 3.9.
SAMtools 1.17 includes a new samtools reset subcommand, a cram-size subcommand that writes out metrics about a CRAM file, a --sanitize option to fixmate and view that fixes common mistakes made by aligners, a CRAM_OPT_REQUIRED_FIELDS option for view -c for significant speed improvements, new --excl-flags --incl-flags and --require-flags in samtools depth, a Consensus --mark-ins option that allows consensus output to include a markup indicating the next base is an insertion, and a number of performance improvements.
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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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