It's our first newsletter of 2020, and as we prepare to make the leap into February, with one extra day of work this leap year, we have news for you, with our latest webinar posted online and the start of our 2020 lineup, an SBGrid member tale focused on Guy Schoehn at IBS Grenoble, technology updates galore, as we prepare to test a new software installer and dodge the latest curve balls Apple has thrown. We've got 11 software updates, 2 new titles, 3 new SBGrid members, and 3 member publication highlights. Onward.
In our Tuesday webinar we got a primer on VMD from John Stone and Abhishek Singharoy, which you can now watch on the SBGrid YouTube channel. We've got speakers lined up through May, so be sure to mark you calendars, and as always, let us know if you'd like to hear more from a particular developer:
- February 11: Schrodinger Intro to Structure-Based Drug Design with Jennifer Chambers
- March 3: Cinderella with Thorsten Wagner
- April 7: Phenix/DivCon with Lance Westerhoff,
- May 5: XDS with Kay Diederichs
For our January SBGrid Member Tale, we heard from Guy Schoehn who believes in the power of yes to get science done. Schoehn began his work using cryoEM in the mid-1990s and now heads the Methods and Electron Microscopy group at Institut de Biologie Structurale in Grenoble, France where he oversees three teams, manages the technical platform, lends his EM expertise in collaborations with over a dozen different groups, and dabbles in a bit of EM art. [Read the full story].
We have lots of technology updates for you this month, with some significant reworking of things thanks to Mac Catalina, the new version of CentOS testing underway, and a spiffy new version of our installation client for beta testing:
Beta testers needed for new SBGrid command-line installation client. We're looking for a few good beta testers for the next version of our command-line installation client on Linux and MacOS. If you're interested, drop us a line at firstname.lastname@example.org.
CentOS 8 support coming soon. We've had a few users itching to upgrade to CentOS 8, and most packages will probably work as expected, but there are a few known issues we need to address. We plan to make CentOS 8 support official on March 1, and your feedback is helpful, so please let us know if you are using CentOS 8 or plan to update in the near future. Email us at email@example.com.
/programs is moving to /opt/sbgrid. To support new releases of MacOS and better support Linux environments where additions to / are problematic, the root of SBGrid's software collection is moving. Its new home: /opt/sbgrid. There’s nothing for you to do now, but we’ll soon have a symlink from /opt/sbgrid to the current installation directory and eventually the old /programs path will be unnecessary. This task is a big one that we hope to complete by spring. More info next time around.
MacOS 10.15 workaround. Apple’s update to 10.15 Catalina introduced major changes to MacOS, including dropping support for 32-bit applications and a read-only filesystem root that makes adding /programs impossible. We recommend delaying an upgrade to Catalina if possible, but for those who already have Catalina, we do have a temporary solution and 64-bit software works as expected. For more information on
We'll drop the workaround requirement this spring when the move to /opt/sbgrid is complete.
Our latest software push includes updates toautoPROC, BLAST+, Bsoft, BUSTER, CCP-NMR, ChimeraX, crYOLO, ISOLDE, Phenix/DivCon, R, SIMPLE, along with two new titles: 3DFSC and Anvi'o. See Software Changes below for complete details.
January brought us three new SBGrid members, Frédéric Allain from ETH Zurich, and two new labs at Vanderbilt University: William Wan and Qiangjun Zhou. Welcome to our newest members!
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:
The University of Chicago's Demet Araç-Özkan, Tobin R. Sosnick, and Minglei Zhao coauthor a paper in Nature Communications where they present the solved structure of the extracellular regions (ECRs) of adhesion G protein-coupled receptors (aGPCRs) Gpr126 and employ alternative splicing to elucidate the mechanisms governing their function and regulation. [Abstract]
In Biological Psychiatry, Aashish Manglik of the University of California, San Francisco, details what we know about the molecular pathway of opioid activation and response to facilitate the discovery of new targets for the development of novel opioid medications that have a lower risk of addiction and lethality. [Abstract]
From our graduate student desk, Harvard student Kristen Rodrigues highlighted a publication from the laboratory ofUhn-Soo Cho that appeared this month in Nature Communications, and improves our understanding of chromatin-interacting protein complexes in mixed lineage leukemia. [Read more].
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:
Structural biology applications used in this project were compiled and configured by SBGrid .
 A. Morin, B. Eisenbraun, J. Key, P. C. Sanschagrin, M. A. Timony, M. Ottaviano, and P. Sliz, “Collaboration gets the most out of software.,” Elife, vol. 2, p. e01456, Sep. 2013.
3DFSC is new to SBGrid, at version 3.0. 3DFSC quantifies directional resolution and density isotropy of cryoEM maps using a 3D Fourier Shell Correlation (FSC) algorithm.
Anvi'o was added to SBGrid at version 6.1. Anvi'o is an open-source, community driven analysis and visualization platform for microbial ‘omics.
autoPROC's latest update - version 20191129 - includes support for XDS with keywords SNRC and BATCHSIZE, improved handling of overloaded reflections in the AIMLESS-only scaling path, better handling of explicitly excluded images (keyword EXCLUDE_DATA_RANGE XDS), a bug fix in the Dectris/Neggia plugin to correctly handle 16-bit Eiger HDF5 datasets, improvements in detecting Eiger data in mini-cbf format, and a fix to the HDF5-to-mini-cbf converter (hdf2mini-cbf) to correctly determine and output the Count_cutoff value from HDF5 into the mini-cbf files.
BLAST+ 2.10.0 is now available and offers updated composition-based statistics for protein-protein comparisons and an experimental Adaptive Composition Based Statistics option that increases the likelihood of finding novel results. To enable this option set the environment variable ADAPTIVE_CBS to 1.
Bsoft is now at version 2.0.6
BUSTER version 20191129 includes a change to Pipedream so that ,when run from images or from output of a previous autoPROC job, it will use the anisotropically analyzed and scaled output file from STARANISO for all further steps. Users will also notice improvements to aB_hydrogenate to ensure disulfide bridges are not accidentally hydrogenated when they involve symmetry or are at large distance, to handling of resolution limits, several improvements to Grade, along with many other bug fixes and performance improvements.
CCP-NMR was updated to version 3.0.0, described as a modern, flexible, fully reworked version of the CcpNmr Analysis 2.4 software for Biomolecular NMR that contains modules for Assignment, Metabolomics and Screening, with a Structure module in development.
ChimeraX version 0.91 is the new default. This update includes new graphical interfaces for Rotamers, Clashes, Contacts, and H-Bonds, a tape-measure mouse mode to measure distances, multiple sequence alignment from Blast Protein results, VR status and settings saved in sessions, augmented-reality video capture, a Maestro file reader available from Toolshed, improved MLP parameters for showing protein hydrophobicity, a medical Image toolbar, new Segger tools: Segment Map watershed segmentation, Fit to Segments,
Fit in Map graphical interface, an option for users to create their own presets, animation options for 2D labels can be animated, and a new Map Eraser tool and Measure and Color Blobs tool.
crYOLO 1.5.5 is now available. With this update the developers have added the –use_multithreading option for training, for use when python multiprocessing leads to problems during training (e.g. freezing, dying workers). Internal refactoring was also done to accommodate Boxmanager 1.2.8, which integrates a low pass filter to make training data creation easier.
ISOLDE was updated to 1.0b4, to coincide with the stable release of ChimeraX 0.91. This version integrates with the ChimeraX session save/restore framework, adds new adaptive torsion restraint implementation to restrain protein torsions to their current geometry or to a reference model, integrates ISOLDE documentation with the ChimeraX documentation framework, adds support for multiple independent sets of adaptive distance restraints, and includes a number of other performance improvements. ISOLDE source is also now available on GitHub.
Phenix/DivCon was updated to vDEV.618. In this version the MovableType (MT) tutorials were updated to include additional execution scenarios, the MT-GARF [statistical] potential is used throughout MT by default, but users can use the “-h amberff14” argument to select MT-AMBER instead, and several other performance improvements are included.
R was updated to 3.6.2 (Dark and Stormy Night). See the R archives for detailed release notes.
SIMPLE has a new 3.0 beta release with a new graphical user interface.
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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