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Dear Consortium Members and Affiliates,
The new academic season is upon us, and with that comes a new season of software webinars along with our usual updates, including a software push with 12 updates, 4 new members to welcome, and 2 member publication highlights.
Our new season of software webinars is coming together nicely. We have a few spots left to fill, so if there is a software title you'd like to learn more about, please let us know. You can see complete details on our website - https://sbgrid.org/webinars/ - and we'll soon add an option to register. You can also find recordings from many of our past webinars on the SBGrid YouTube channel.
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Software updates were pushed out for twelve titles: autoPROC, BUSTER, CCP4, Coot, CP2K, DeepEMhancer, Global Phasing Suite, MotionCor2, Muscle, PDBFixer, and RELION. See Software Changes below for complete details.
The month of August brought five new members: Michael Malkowski, D. Fernando Estrada, and Andrew Gulick from University of Buffalo, the CryoEM Facility at HHMI led by Zhiheng Yu, and Douglas Kojetin of Vanderbilt University. Welcome to our newest members!
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Member Publications Highlights |
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FROM OUR GRADUATE STUDENT DESK 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.
CITE 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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Software Changes |
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autoPROC 20230726 will now include the number of consecutive images present in the datablock describing the settings of the first image, has new options when using aP_select_pdb to control amplitudes using autoPROC_SelectPdb_UseEvalues and setting autoPROC_SelectPdb_CellDiff_UseCorrespondingMtz to "yes" will also use amplitudes from MTZ file instead of computing them afresh from a PDB file, an option to report settings supplied by non-standard macros in stdout and summary.html by setting autoPROC_ReportNonStandardMacros="yes".
BUSTER 20230726 includes documentation improvements when the "ana_ssbond" tool runs with at least two "-v" arguments it now provides a table and details for each considered SS-bond. Also new: better error messaging when encountering duplicated bond restraints, a new default to use OS-provided Gnuplot binaries when available to improve runtime, and a new montage of plots from Pipedream to highlight the progress of the overall refinement process before and after ligand fitting.
CCP4 8.0.012 is the new default.
COOT 0.9.8.91 is the stand alone version of coot, updated with several new features including options to use add_hydrogen_atoms_to_residue() in mutate_internal() if the residue has hydrogen atoms, add add_hydrogen_atoms_to_residue() to the API, allow the addition of hydrogen atoms to nitrogen atoms with energy type NR5, and to remove the Biscu-it QED interface, along with fixes for a number of bugs.
CP2K 2023.2. See the version history for full details
DeepEMhancer .16 is available via version override and corrects a problem when using it with Tensorflow. Note: this new version requires users to download new models: deepemhancer --download.
MotionCor2 1.6.4 is the new default.
Muscle was bumped a couple of releases to version 5.1. The update to Muscle5 is a major re-write of MUSCLE based on new algorithms to be more accurate, often faster, and scaling to much larger datasets.
PDBFixer 1.9 contains optimizations and minor feature updates. It is designed to work with OpenMM 8.0 RELION 4.0.1 includes support for MRC movies compressed by bzip2, xz or ZStandard in RELION's motion correction and Bayesian Polish for SPA using the pbzip2, xz or zstd commands, repair of C10 to C19 point groups, a fix to the CTF-premultiplication flag upon re-extraction, a repair to the implicit 3.0 to 3.1 STAR format conversion, support for the latest CTFFIND, and a memory issue fix.
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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 https://sbgrid.org Report software bugs: sbgrid.org/bugs
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