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Dear Consortium Members and Affiliates,
Fall colors are still painting our horizons here in New England, as we head into November with the latest SBGrid updates. We have webinars on the horizon too, with 3 talks scheduled for November in our regular series, 4 more in our SBGrid-Australasian mini-series, and 3 webinars from last month posted to YouTube. Also this month, there is a story featuring Baylor College of Medicine Professor Ming Zhou, 8 software updates and 2 new titles, nine new members to welcome, and 3 member publication highlights.
Our regular webinar series continued in October with some terrific science talks from Arthur Neuberger and Kirill Nadezhdin in Alexander Sobolevsky's laboratory at Columbia University and Johannes Elferich in Niko Grigorieff's laboratory at University of Massachusetts Medical School. Our own Jim Vincent also gave a tutorial focused on how to access BioGrids, for those SBGrid laboratories that have opted in to receive the BioGrids software stack. Recordings of these presentations are available on the SBGrid YouTube channel. |
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This week we were excited to host Prof. Yifan Cheng as the first speaker in a series of presentations timed for our members in New Zealand, Australia, and Asia, and organized in collaboration with Prof. Kurt Krause at the University of Otago and Prof. Antoine van Oijen from University of Wollongong and ARC CCeMMP. This series of 5 talks is focused on CryoEM: from Sample to Structure and is open to all. Times posted are for New Zealand and please note that we may not be able to record these talks.
For our October SBGrid Tale, we talked with Ming Zhou from Baylor College of Medicine in Houston, who shared some of his feelings about fat. Zhou looks at fat from all sides, how it is absorbed, broken down, and deposited, acting as an energy source, fueling tumor growth, impacting heart disease, and contributing to that pesky belly bulge. From his studies on DGAT1 enzymes that help assemble triglycerides and SCD1's role in saturated fat transformation to his plans for examining the role of bile acids in cholesterol consumption and how lipids and proteins interact, Zhou is fleshing out the facts about fat. [Read the full story].
Our monthly software push includes updates to autoPROC, BUSTER, crYOLO, Phenix, R, RELION, samtools, and Topaz along with two applications new to SBGrid: starfile and VESPER. See Software Changes below for complete details.
October was a busy month, with nine new laboratories joining SBGrid, including Christopher Barnes from Stanford University, Jeffrey Holt from Boston Children's Hospital, Sam Light from University of Chicago, Richard Hite, Melinda Diver, and Stewart Shuman from Memorial Sloan Kettering Cancer Center, and Allison Williams at University of California, San Francisco. We also have two new members from institutions that are new to SBGrid: Diane Joseph-McCarthy at Boston University and Tom Seegar from the University of Cincinnati College of Medicine. Welcome to our newest members!
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Technical notes from our Software Team |
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On October 25th Apple released macOS Monterey. As always, we recommend waiting on OS upgrades until software developers have had a chance to work out the bugs. In our limited preliminary testing SBGrid applications appear to work as expected, including the SBGrid installation manager, but we do anticipate that updating to Monterey will cause problems with some applications. Waiting to update production systems is the safe way to go.
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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:
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 3 new citations in the month of October, in publications with contributions from these SBGrid-member laboratories: Juan Fontecilla-Camps from University of Grenoble Alpes in ACS Chemical Biology: Transient Formation of a Second Active Site Cavity during Quinolinic Acid Synthesis by NadA; Emil Pai of University of Toronto in ChemBioChem: Defluorination Capability of l-2-Haloacid Dehalogenases in the HAD-Like Hydrolase Superfamily Correlates with Active Site Compactness; and Oliver Ernst of University of Toronto in Structure: Structural evidence for visual arrestin priming via complexation of phosphoinositols.
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Software Changes |
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autoPROC version 20211020 includes improvements to the initial indexing when no SG/cell is given, introducing a series of fall-back options to help with really poor diffraction patterns, and to the analysis of found/indexed spots. There is new support for removal of potentially spurious (weak) spots using the parameter autoPROC_CleanupSpots_RemoveLowestNum (default=0), for ReverseRotationAxis=yes setting even for datasets in d*TREK format, and for compressed (gz, bz2) image processing for d*TREK (Rigaku) formatted images. MASSIF-1/ESRF settings were added for kapparot.sites, to process datasets collected on MASSIF-1 that make use of the Kappa goniostat. There is better control of the indexing process when encountering Pilatus or Eiger detectors with two new parameters (autoPROC_Img2Xds_Pilatus_MaxErrorSpotPosition=2.0 and autoPROC_Img2Xds_Eiger_MaxErrorSpotPosition=4.0 can), and a new fallback option when scaling fails due to over-optimistic crystal-detector distance.
BUSTER 20211020 adds support for double-quotes (") in atom names within the restraint dictionary handling of Grade, Rhofit and BUSTER and for user-defined restraint dictionary location to geometry-only refinement, a fix to the handling of user-provided restraint dictionaries to support compound names like "%01," and to MakeLINK in generating connectivity information, with new support for CRO residue and improved automatic determination of residue class. There are fixes for problems with aB_fuseplanes tool and Grade2 dictionaries, to water molecule counting within the "analyse" tool, and to buster-report to better support MapOnly-refinements.
crYOLO 1.8-b40 is a beta version available via version override. It adds a picking mode for tomography that works with single particles and filaments. The developers caution users that retraining is needed when using this new feature with old filament models. Also new: CBOX files are now written in the STAR format and users can use .star files as input during prediction.
ICM Browser Pro was updated to version 3.9.2c.
Phenix dev-4379 nightly build is available via version override.
R 4.1 is out with a couple notable new features. This version introduces a pipe operator |> into the base R syntax, which requires the presence of parentheses. Also new is shorthand syntax to make anonymous function declarations more succinct. The developers include a reminder that if you use new syntax introduced in R-4.1, your code will not run on previous versions of R.
RELION 4.0-beta-2 was pushed out and is available via version override.
samtools 1.14 removes the legacy samtools API (libbam.a, bam_endian.h, sam.h and most of bam.h), includes the samtools samples command to list the samples used in a SAM/BAM/CRAM file, and updated mpileup to support base modifications via the SAM Mm/…
starfile version 0.4.9 was just added to SBGrid. starfile is a Python implementation of the STAR file format, designed principally for compatibility with RELION format STAR files, whch allows users to create and easily open STAR files using a simple API, exposing data blocks as pandas DataFrame objects.
Topaz update 2.5.0_2 is available.
VESPER is also new to SBGrid at version 20210908. VESPER uses a vector -based algorithm to accurately identify the global and local alignment of cryoEM maps.
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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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