Dear Consortium Members and Affiliates,
We're keeping it trim for our July monthly update, with our webinar series on hold for the summer, but other bits still chugging along including a software release with nine updates and four new titles, three new members to welcome, and two student publication highlights.
Our webinar series is on hold for the summer months, but we are beginning to set the lineup for next year, so please be sure to let us know if there are software titles you'd like to hear more about. In the meantime, you can find a collection of many of our past webinars on the SBGrid YouTube channel.
Our July software push includes updates to autoPROC, BioXTAS RAW, Buster, Chimera, EMAN2, Julia, POKY, Phenix, and SHELX-2013, along with these four new titles: AF2Complex, fidder, MemBrain-Seg, and RFdiffusion. See Software Changes below for complete details.
We had three new members join in the month of July: Craig Smith of Washington University in St. Louis, the Stanford-SLAC Cryo-EM Center, and Eva Kowalinski of EMBL Grenoble. Welcome to our newest members!
Member Publications Highlights
FROM OUR GRADUATE STUDENT DESK
Over 90 new member publications appeared in journals this month. You can find a 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 SBGridSBGrid operations are funded with member fees and grants, so we are grateful when you are able to acknowledge SBGrid in your presentations and publications.
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:
SBGrid's eLife paper received 4 new citations in the month of July, from these SBGrid-member laboratories: Dirk Slotboom from University of Groningen in Nature Communications: Expulsion mechanism of the substrate-translocating subunit in ECF transporters; James Letts from University of California, Davis in Nature Plants: Plant-specific features of respiratory supercomplex I + III2 from Vigna radiata;
M. Gordon Joyce of U.S. Military HIV Research Program in Journal of Virology
Targeting the Spike Receptor Binding Domain Class V Cryptic Epitope by an Antibody with Pan-Sarbecovirus Activity; and Marc Kvansakul of La Trobe University in Nature Communications Biology: Membrane recruitment of the polarity protein Scribble by the cell adhesion receptor TMIGD1
AF2Complex is new to the SBGrid collection 1.4.0. AF2Complex is a tool for predicting and modeling protein complexes with deep learning.
autoPROC 14.06.2023 was pushed out with several improvements. You'll notice a new count of the images present in any given set of consecutive images in the datablock that describes the settings of the first image, new options in aP_select_pdb including using amplitudes instead of normalized structure factors by setting autoPROC_SelectPdb_UseEvalues parameter "no" and setting autoPROC_SelectPdb_CellDiff_UseCorrespondingMtz to "yes" to also use amplitudes from MTZ file instead of computing them afresh from a PDB file. Also new is an autoPROC_ReportNonStandardMacros setting to provide information about settings supplied by non-standard macros.
BioXTAS RAW 2.2.1 fixed a bug that prevented some calibration and masking operations from being used.
Buster 20230614 includes a new option to get a table and details for each considered SS-bond using "ana_ssbond" with at least two "-v" arguments, better error messaging for duplicated bond restraints, a new process to take advantage of the faster runtime of OS-provided Gnuplot binaries, and an update to Pipedream to generate a montage of plots to highlight the progress of the overall refinement process before and after ligand fitting.
Chimera was updated to 1.17.1 for Mac and 1.17.2 for Linux and includes a new option to use the File→Export Scene menu item to export the Chimera scene for use in ChimeraX, creating a Python file (.py suffix) that can be opened in ChimeraX. Also of note: because the Opal web service infrastructure on UCSF RBVI servers is obsolete, many services were ported over to use the newer web service infrastructure used by ChimeraX. Services that were not possible to port: Anchor Graph, CDK Depiction, MDA BlastP, MultiFit, SAXS/SAXS2.
EMAN2 2.99.52 is the latest nightly build, now available via version override.
fidder is another new tool in the SBGrid collection at version 0.0.8. fidder is a Python package for detecting and erasing gold fiducials in cryo-EM images.
Julia 1.9.1 was pushed out.
POKY is now at 20230511
MemBrain-Seg e28baac was added to the SBGrid collection. MemBrain-Seg is a reliable method for segmenting membranes in 3D microscopic images for cryo-electron tomography (cryo-ET).
Phenix was updated with the latest nightly build - 1.21rc1-4985, which is available via version override
RFdiffusion 1.1.0 is new to SBGrid RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges.
SHELX-2013 was updated to the latest release.
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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