Dear Consortium Members and Affiliates,
March brought some fun news for the SBGrid team, as our member count topped 400. In these uncertain times it is great to have such broad support from the community! In other news, you'll find new webinars on our YouTube channel and the April lineup below, a big software push with 16 updates and 1 new title, some technical notes on XQuartz, a call for beta testers to try out our new installation manager, new position postings from Daniel Panne's lab and Vanderbilt's Center for Structural Biology, 5 new members to welcome, and 3 member publication highlights. Read on for details!
Many thanks to our March webinar presenters. You'll find recordings on our SBGrid YouTube channel from Willy Wriggers on SITUS along with updates on recent research from Marcos Sotomayor of Ohio State University, Woody Sherman at Silicon Therapeutics, and Daniela Fera of Swarthmore. We also heard from Florent Delhommel of Michael Sattler's group at Technical University of Munich and and hope to make his talk available soon.
Our most recent software push includes 16 updates - autoPROC, BLAST+, BUSTER, CCP4, CryoAssess, DIALS, EMAN2, Global Phasing Suite, GPU ISAC, IGV, PyEM, Rosetta, SAMtools, Schrodinger, Scipion, XDS - and one new title: RELION realtime preview. See Software Changes below for complete details.
In March 5 new members joined SBGrid, which brings us to over 400 members in 23 countries, including Natalia Jura of University of California, San Francisco, Baron Chanda and Wayland Cheng of Washington University St. Louis, Niels Volkmann of Insitut Pasteur, and Benoit Roux from University of Chicago. Welcome to our newest members!
Technical notes from our Software Team
XQuartz version 2.8: On macOS, many SBGrid-supported applications require XQuartz. Version 2.8 was released on 2021-03-21 and corrects a number of issues present in the beta and RC releases. This version is the first release with native Apple Silicon support. Applications like COOT and ADXV appear to work normally with this latest release, though we have observed long launch times for XQuartz on Catalina and Big Sur. You may need to
Daniel Panne's group at the University of Leicester has posted a position for a Postdoc -- Structural Biology of Genome Regulation. The Panne group focuses on signal processing on enhancers and how 3D genome organization contributes to various aspects of genome function. The successful candidates will use a multi-disciplinary approach that includes preparative biochemistry of multi-protein complexes, protein engineering and state-of-the-art biophysical and structural techniques. Contact email@example.com for additional information and [full details].
The Center for Structural Biology at Vanderbilt has posted a position for a Staff Scientist to support high performance computing and storage needs for CSB investigators. This position will focus on optimizing software installs, data management, scripting, and user support for the CSB research community in order to streamline workflows that utilize Vanderbilt’s growing HPC and data storage facilities [full details].
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:
SBGrid citations: SBGrid's eLife paper received 5 new citations in the month of March, from these SBGrid-member laboratories:
Ryan Hibbs from University of Texas Southwestern Medical Center in Cell: Structure and gating mechanism of the α7 nicotinic acetylcholine receptor; Hao Wu at Boston Children's Hostpial in Nature: DPP9 sequesters the C terminus of NLRP1 to repress inflammasome activation; Mark Carr at the University of Leicester in Cytokine: Conformational dynamics in interleukin 17A and 17F functional complexes is a key determinant of receptor A affinity and specificity; and John Tainer of MD Anderson Cancer Center in two new publications, Progress in Biophysics and Molecular Biology: Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors and An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation.
autoPROC 202102224 includes a new option to automatically detect very poor image ranges and exclude them from processing, the new do_setup=no setting to turn off automatic extraction of site-specific processing options via dataset metadata, a new tool (aP_anaspot) to enhance the analysis of initial and indexed spots, improvements to iterative indexing that to cover and highlight when more than 360 degrees of data are collected, better accommodation of datasets with ice-rings and/or damaged pixels, along with other improvements detailed in the link to the release above. The developers also encourage users to directly upload to the PDB the mmCIF files produced in autoPROC, which utilize dictionary items incorporated in the official PDB Exchange.
BLAST+ 2.11 has a new feature that allows threading by query batch in rpsblast/rpstblastn. Enabling this option using -m t provides more efficient searching with large numbers of queries. Important bug fixes in this release include removing the need for an internet connection for the blast_formatter and, for Windows systems, makeblastdb no longer requires as much virtual memory and produces smaller LMDB files. See the release notes for details on more improvements and bug fixes.
BUSTER 20210224 includes a big update to Pipedream pre-Rhofit refinement protocols to separate the addition of solvent from the process of ligand density elicitation (the -L protocol in BUSTER) while providing a framework for future refinement strategies. Pipedream will also report the number, approximate volume, and location of potential ligand sites located using the -L option, and the number of waters present after pre-Rhofit refinement and post-refinement steps. Users can now specify residues that should be ignored during the generation of occupancy-refinement specifications using pdb2occ, have finer control over the handling of hydrogens already present in the input model with "hydrogenate" and "aB_hydrogenate" commands, and may notice an improvement to handling of non-standard amino-acid hydrogenation in aB_hydrogenate. The developers also encourage users to directly upload to the PDB the mmCIF files produced in BUSTER, which utilize dictionary items incorporated in the official PDB Exchange.
CCP4 7.1.012 includes updates to ample, ccp4cloud, ccp4i2, crank2, mrbump, pointless, and simbad.
DIALS 3.4.0 includes updates to dials.integrate so that more reflections qualify for profile fitting, dials.scale has an added outlier rejection based on normalized intensities and fixes an error model issue, dials.image_viewer has a new basis_vector_scale= parameter to adjust the length of the basis vector overlay and fixes various display issues relating to viewing still images, dials.reciprocal_lattice_viewer added an option to label the reciprocal lattice point nearest the centre, dials.background adds the option output.plot= to save an image to disk instead of showing interactively, dials.background fixes crashes when writing an output plot with bad display configuration, dials.estimate_resolution will reject Wilson outliers to minimize the effect of spurious observations, like ice rings, on the resulting resolution estimates, dials.import allows selection of individual components of a reference model using use_beam_reference=, use_gonio_reference= and use_detector_reference=, dials.merge adds an option to set wavelength_tolerance for MAD datasets, and dxtbx has improved support for Timepix 2M (cctbx/dxtbx#298), SwissFEL Jungfrau 16M (cctbx/dxtbx#303), and Eiger 16M XE at Diamond (cctbx/dxtbx#323) detectors.
EMAN2 2.91 is a bug fix release.
Global Phasing Suite was updated to version 20210224. This suite is available to industry members who are Global Phasing Consortium members.
GPU ISAC was updated to version 2.3.4.
IGV 2.9.4 is the new default. With the bump to 2.9, batch execution got an overhaul with major performance improvements, a new colorBy batch command to control coloring of alignments, new commands to control the sequence track (setSequenceStrand and setShowSequenceTranslation), and an option to respect maxPanelHeight when creating snapshots. Users may also notice a new alignment track menu item to copy a clipped read sequence, the ability to group alignments by reference concordance, and changing the track color for feature tracks now supports setting different colors for the positive and negative strands.
PyEM was updated to 20210211.
RELION realtime preview 20200204. New to SBGrid, RELION realtime preview is a simple python script that allows users to follow the progress of 2D/3D classification and refinement in RELION in real time.
Rosetta was bumped to release 2021.07
SAMtools version 1.12 include improvements to detection of I/O errors and record parsing errors during the reading of SAM/BAM/CRAM files, the addition of new targets -- -check-all, test-all, distclean-all, mostlyclean-all, testclean-all -- which allow SAMtools installations to call corresponding Makefile targets from embedded HTSlib installations, --version now displays a summary of the compilation details and available features, including flags, used libraries and enabled plugins from HTSlib, the legacy samtools API was deprecated and the developers recommend coding against the HTSlib API directly, a new FASTA/FASTQ sanitizer script (fasta-sanitize.pl) was added, CI scripts were updated to recurse the HTSlib submodules when cloning HTSlib, to accommodate for the CRAM codecs.
samtools stats now counts only the filtered alignments that overlap target regions, if any are specified, displays the number of supplementary reads in the SN section and supplementary reads are no longer considered when splitting read pairs by orientation (inward, outward, other).
samtools view now accepts option -N, which takes a file containing read names of interest, the -d option to work without a tag associated value, -d and -D options now accept integer and single character values associated with tags, not just strings, and it works with filtering expressions introduced by HTSlib with the filtering expression passed using the specific option -e or the global long option --input-fmt-option.
samtools markdup perfomance is increased when a single read has tens or hundreds of thousands of duplicates.
Schrodinger was updated to version 2021-1
Scipion 3.0.9 includes support for ChimeraX.
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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