News from SBGrid is coming your way, on another hot summer day in Boston, with a profile on SBGrid member Marco Sotomayor, the latest webinar news, a big software push with 17 updates and 2 new titles, a position posting from U Wisconsin National Magnetic Resonance Facility, 2 new members to welcome, and 3 member publication highlights. Keep cool and read on.
For our July SBGrid Tale, we made our way to the Heartland to hear from Marcos Sotomayor at Ohio State University, and hearing is at the heart of his research. With a long term focus on understanding the tip links that make hearing possible, Sotomayor is now extrapolating what he has learned to understand proteins that link cells together in other diseases. Read the full story.
Last week's webinar, featuring Colin Palmer on Model building and validation in CCP-EM is now up on the SBGrid YouTube channel. We're taking a summer break in August, but webinars will resume in the fall, so mark your calendars and let us know if you would like to hear more on a particular title:
- September 24: ISOLDE with Tristan Croll
- October: waiting for your suggestions...
- November 12: EMAN2 with Steven Ludtke
- December 10: Cinderella with Thorsten Wagner
- January: VMD with John Stone and David Hardy
The July software push includes new versions of autoPROC, BioXTAS RAW, BUSTER, CCP4, CCP-EM, ChimeraX, DSSR, DynDom, Geneious, GPHL, Molprobity, NMRFx Processor, Phenix, PyMOL, RELION, Schrodinger, and Topaz. We also added two new titles: Durin (an XDS plugin) and ISOLDE. See Software Changes below for complete details.
A Postdoctoral Research Associate position is open at the University of Wisconsin, Madison National Magnetic Resonance Facility. You can find more details on the SBGrid Member Position Postings page of our website.
July brought two new members to SBGrid: Dirk Slotboom is our second member at the University of Groningen and James Crowe our 17th at Vanderbilt University. Welcome to our newest members!
Member Publications
Over 90 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:
- Available online in eLife this month is a new paper that Maofu Liao of Harvard Medical School co-authored that looks to uncover how ferritin deficient organisms store iron. Studying Quasibacillus thermotolerans, the researchers discovered the huge iron storage capacity of the encapsulin compartment of Q. thermotolerans, lending support to idea that encapsulins act as microbial storage units for iron. [Abstract]
- Straining to get better from that influenza virus? A new publication in Nature Microbiology, from the lab off Yi Ren at Vanderbilt University, identifies mRNA export receptor complex NXF1–NXT1 as the target of viral virulence factor NS1. The authors reveal that a mutant influenza strain unable to bind NXF1– NXT1 is unsuccessful in blocking host nuclear mRNA export, significant because of its role in the release of mRNAs encoding antiviral factors. Elucidating the target of NS1 and the molecular pathway of viral inhibition of host mRNA export could aid in the development of therapeutics to neutralize NS1 (and potentially the influenza virus) and boost host immunity. [Abstract]
- From our graduate student desk, Harvard student Kristen Rodrigues highlights a publication from the laboratory of Feng Zheng at MIT in which researchers investigated a CAST from Scytonema hofmanni, to understand the mechanism of RNA-guided DNA transposition, and engineered CAST to more precisely insert DNA without relying on the cell's ability to repair itself. 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 [1].
[1] 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.
Link to article: https://elifesciences.org/articles/01456.
SBGrid's eLife paper received 9 new citations in July, from these SBGrid-member labs:
- Melanie Ohi at University of Michigan and Borden Lacey from Vanderbilt in eLife.
- Christopher Fromme from Cornell University in bioRxiv.
- Holger Sondermann at Cornell University in eLife.
- Eric Girard at IBS Grenoble in the Journal of Applied Crystallography.
- Andrew Kruse and Piotr Sliz from Harvard Medical School in bioRxiv.
- Catherine Drennan of MIT in Journal of Biological Chemistry.
- Karen Anderson from Yale University School of Medicine in Protein Science.
- Marc Kvansakul at La Trobe University in The FEBS Journal.
- Navtej Toor at NIH in Cell. [Abstract]
Software Changes
autoPROC was bumped a couple of versions to 20190607. With this version you'll find support for neutron data from the D19 instrument at the Institut Laue-Langevin (ILL), improved handling of HDF5 datasets (within find_images) with smaller *_master.h5 files, the addition of Gemmi binary ("gemmi") to the autoPROC standalone distribution, improvements to HDF5 file location handling, updates to XDS, and a new parameter - autoPROC_CadSysAb - to allow carry through for systematic absences (as far as possible) within autoPROC.
BioXTAS RAW version 1.6.0 includes several major changes: Completely new and improved SEC-SAXS processing, including increased speed, new automated buffer and sample region selection and baseline correction. BIFT was overhauled with many bug fixes and the addition of Monte Carlo error estimation and extrapolation fit of data to I(0). RAW now preserves matching metadata across processes, which is saved with keywords compatible with the SASBDB. Users can also provide arbitrary metadata during data reduction. All new icons are compatible with retina displays, on start up, RAW now loads the last used config, rather than the last saved config, and users can now open any analysis window (Guinier, MW, GNOM, etc) multiple times for side-by-side processing of data sets.
BUSTER was updated to 20190607, which fixes automatic adjustment of X-Ray weights and the DFc completion feature. You can find improvements to the generation of TER records in PDB files and treatment of ligands with a highly connected network of bonds. The update to sftools in CCP4 (7.0.073) offers broader support for more space groups. There is a new check in "fetch_PDB" to handle problematic deposited reflection data and the automatic X-Ray weight adjustment will now only look at the rms(bond) value for standard protein residues.
CCP4 version 7.0.076 includes updates to output of mmcif for deposition in Refmac, and in ccp4i2, an update to deposition and to MR.BUMP task.
CCP-EM was updated to the latest nightly release: 20190722
ChimeraX version 0.9 is now available. You can find a full list of recent updates in the changelog.
DSSR version 1.9.4-20190708 is out, with revised criteria for Watston-Crick pairs, improved identification of loops in rare cases, an updated DSSR User Manual, and miscellaneous code refinements.
Durin 2019v1 was just added to the collection. Durin is an XDS plugin for reading HDF5 files following the NeXuS format or those written by Dectris Eiger detectors.
DynDom is now at version 1.04.
Geneious version 2019.2.1 includes a new Vector new Vector NTI Express Database importer (beta)NTI database importer and allows drag and drop import, options to automatically design primers for tiled Sanger Sequencing, and improved Text View formatting of Sequences and Alignments, now supporting formatting and export of sequences in accordance with U.S. Patent Office requirements, formating sequences into blocks of residues separated by gaps, and options to specify regions of a sequence to translate.
GPHL was updated to 20190607 for our industry users who have a license.
ISOLDE is new to SBGrid. ISOLDE is a modern, immersive environment designed to ease the historically challenging task of building high-quality macromolecular models into low to medium resolution experimental maps. ISOLDE installed as a UCSF ChimeraX plug-in.
Molprobity 4.4 is now available for Linux.
NMRFx Processor was bumped several versions 10.3.34. See a full changelog for details.
Phenix nightly build 1.16-3549 is out, with a new GUI for mmtbx.prepare_pdb_deposition to make mmCIF files for deposition into the PDB, a new tool for getting a validation report from the PDB (phenix.get_pdb_validation_report), added sequence checking to Comprehensive Validation for Cryo-EM, and Amber functionality available by default.
PyMOL is now at version 2.3.1 (Incentive PyMOL) and includes atom-level cartoon transparency, fast MMTF export, a new display gaps (seq_view_gap_mode) mode in Sequence viewer, a builder panel for nucleotides, APBS plugin support for RNA out-of-the box, and MAE user label support.
RELION version 3.0.7 is the new default.
Schrodinger version 2019-2 was pushed out. Watch this video to learn about new features in this release.
Topaz was updated to version 0.2.1. With the bump to 0.2 Topaz now supports the newest versions of pytorch (>= 1.0.0). Also new is a denoise command, for denoising micrographs using neural networks, and usability improvements to the GUI.
XDS version 20190606 changes the default setting for the parameter MERGE_TREE=0.2 used in the IDXREF step and the DEFPIX step now accepts a completely vanishing background.
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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