Dear Consortium Members and Affiliates,
The last of the February flurries are falling tonight as we finish our monthly update. Read on for the latest webinar news, 24 software updates and one new title, one new member to welcome, 5 SBGrid citations, and 3 member publication highlights.
We got a primer on the particle picking application TOPAZ in our Tuesday webinar, which is now available to watch on SBGrid's YouTube channel [watch here], and look forward to hosting José-Jesús Fernéndez on April 2nd to learn about the latest developments in TomoAlign and consideration of sample motion in cryoET. Connection details here. Join us!
We got through a little software backlog, pushing out 24 software updates with new versions of ARP/WARP, AutoPROC, BUSTER, CCP4, crYOLO, DIALS, Geneious, GPhL, HKL2000, NAMD, NMRPIPE, PDB Extract, PHENIX, PyMOL, PyRosetta, RELION, Schrodinger, Shelx, Spring, XDS, and XPLOR-NIH. We also pushed out TOPAZ, which users can dabble in while watching the webinar, and the developers tell us to soon expect a new graphical user interface. Stay tuned.
February brought us one new member from Columbia University: Alexander Sobolevsky. Welcome to our newest member!
If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data in the SBGrid Data Bank along with the PDB record deposit and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
SBGrid's eLife paper received 5 new citations in member publications this month, Many thanks to those PIs who remembered to include us in the list of references: John Kuriyan from the University of California, Berkeley in BioRxivv. [Abstract], Gil Privé at the University of Toronto in Communications Biology Abstract], Cornell University's Holger Sondermann in BioRxiv Absract], Evris Gavathiotis of Albert Einstein College of Medicine in Nature Chemical Biology [Abstract], and La Trobe University's Marc Kvansakul in FASEB Journal [Abstract].
Over 40 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple notable highlights below:
- Appearing in Cell is a new paper from Cynthia Wolberger, of Johns Hopkins University School of Medicine, highlighting the cross-talk between H2B ubiquitination and methylation of H3K79 by Dot1L. This study reveals the cryo-EM structures of Dot1L bound to ubiquitinated nucleosome, demonstrates how H2B-Ub stimulates Dot1L activity, and uncovers a role for the histone H4 tail in positioning Dot1L. [Abstract]
- In Nature Chemical Biology, Evripidis Gavathiotis of Albert Einstein College of Medicine reports the discovery of small-molecule BAX inhibitors, known as BAIs, that bind directly to a previously unrecognized pocket on pro-apoptotic BAX, inhibiting BAX activation and, consequently, cell death. These findings denote an advancement in the understanding of BAX and offer a promising schematic for the development of BAX inhibitors for diseases resulting from BAX-dependent cell death. [Abstract]
- From our grad student desk: Harvard student Kristen Rodrigues highlighted a publication from Julie Forman-Kay laboratory that appeared in PNAS in which the authors study the phase separation characteristics of the C-terminal region of the Fragile X Mental Retardation Protein (FMRP), revealing a synaptic activity role in posttranslational modifications. [More on Tumblr]
ARP/WARP is now at version 8.0. This version provides improved performance at resolutions within 2.0-3.5 Å for X-ray crystallography and it is now capable of interpreting cryo-EM maps.
AutoPROC version 20190214 is now available and includes improvements to NeXus-style HDF5 (Eiger2) datasets and initial support for HDF5 datasets with an image number offset.
BUSTER is now at version 20190214 with added support for generating deposition-ready mmCIF files describing the final model, refinement statistics, and restraint dictionaries.
CCP4 updates were pushed out and the new default is 7.0.070.
crYOLO was bumped a couple of versions to 1.2.3. You'll notice the addition of PhosaurusNet to the backend, which makes the patch mode needless for picking single particles; an updated powerful general model, and important bug fixes for the filament mode.
DIALS version 1.12.3 restores the xia2.to_shelx command, fixes character encoding in HTML log, updates dials.export_bitmaps to allow combining output_file with imageset_index, and improves EIGER detector support.
Geneious is now at version 2019.0.4. New features include custom codon usage tables along with several improvement to Sequence View: new statistical calculations, easier options for creating and displaying primers, and new options for directly extracting a PCR product or restriction digested fragment.
GPhL, the installation of Global Phasing for industry members, was also updated to version 20190214.
HKL2000 is now at version 718.
NAMD was bumped to version 2.13, which includes improved GPU performance, with support for non-orthogonal periodic cells, new kernels for bonded force terms, and CUDA support for advanced features.
NMRPipe is now at version 20181211.
PDB Extract version 3.24 is the new default.
PHENIX development version 3374 is now available via version override.
PyMOL version 2.3.0 has a new unified modern user interface - PyQt - that replaces Tcl/Tk and MacPyMOL on all platforms. Also new is better third-party plugin and custom scripting support for Anaconda Python distribution.
PyRosetta version 211 is the new default.
RELION was updated to the stable version of 3.0.
Schrodinger update 2019-1 was pushed out.
SHELX 2019-1 is now available and includes a new version of SHELXE that updates the tracing algorithms with -t1 for fairly high resolution data with a strong phasing signal, -t2 to -t5 for increased times for the initial peptide and alpha-helix searches, and -t6 to -t10 for slower but more effective algorithms. This version also includes a bug fix in -h, a less erratic -z that should be used with caution, improvements to long command lines to avoid buffer overruns, and an option to combine an input fragment in .pda with experimental phases (MRSAD).
Spring was updated to version 0.86.1661 and includes two major upgrades: MICHELIXTRACE for optimized tracing based on statistical thresholding that includes material flexibility analysis of assembly population to survey specimen behavior; and a helical diffraction simulator web service on http://spring.embl.de/ to compute theoretical helical layer line patterns from the input of helical symmetry parameters.
TOPAZ is new to SBGrid, and is a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Learn more.
XPLOR-NIH was bumped to version 2.50. Users will notice improvements to the calcPRE helper program, optimization in Python-level tools for faster script startup, an updated docking script in the dock_dipolar_chemshift example, along with a number of bug fixes and performance improvements and new documentation.
XDS version 20180808 includes improved error handling during the INTEGRATE step and a new input parameter for XSCALE - REIDX_ISET= - which allows reindexing of reflection indices specifically for each input data set.
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.