Dear Consortium Members and Affiliates,
It's time for another SBGrid update, after blowing through July and seeing once again that "summer’s lease hath all too short a date." July news includes an SBGrid visit to Spain and the European Crystallographic Meeting, a profile on SBGrid member Gaya Amarasinghe, a software release with 12 updates and 2 new titles, three new members to welcome, and 3 publication highlights.
If you're traveling to the ECM 2018 in Spain, be sure to stop by the SBGrid poster to ask questions or just say hello. Jason Key, our technical lead, will present and is available for a 30-minute one-on-one for those who have more complex questions. Email us to set up a time.
Gaya Amarasinghe from Washington University at St. Louis is in the spotlight for our July member tale. Amarasinghe reflects on how the subject of his work has changed dramatically - cancer biology in his early studies to the deadly viruses, including Ebola and Marburg, that he studies today - but the questions remain the same as they try to understand the effect on immune signaling cascades. Read the full story.
For our July software release we pushed out updates to 12 titles - ATSAS, CCP4, DIALS, Gromacs, HKL2000, IGV, Jalview, PHENIX, PyMOL, SAMtools, Schrodinger, UltraScan III - and two new titles: crYOLO and ROME System.
July also brought us three new members: Amy Andreotti from Iowa State University, Robert Nolte from GSK, and Priyamvada Acharya from Duke University School of Medicine. Welcome to our newest members!
Member Publications
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.
Thanks to those who remembered to cite SBGrid's eLife paper in July. Adding these new citations to the list - 4 this month - strengthens our grant applications and helps us demonstrate the widespread use of SBGrid in the community. We got a mention from Ryan Hibbs at University of Texas Southwestern Medical Center in Nature [Abstract], Tom Rapoport and Thomas Walz from Harvard Medical School in - Nature Structural and Molecular Biology [Abstract], Phoebe Rice from the University of Chicago in Structure [Abstract], and Harvard Medical School's Danesh Moazed in Nature [Abstract].
More than 40 member publications appeared in journals this month. You can find a complete listing on our website, along with a few notable highlights below:
- Amedeo Caflisch of the University of Zürich has a new publication in The Journal of Physical Chemistry that works to advance our understanding of Alzheimer's disease with simulation studies of Aβ42 peptide. [Abstract].
- Published online this month in AIDS Research and Human Retroviruses is a review by Daniela Fera and her group of excelling undergrads at Swarthmore College, highlighting broadly neutralizing antibodies (bnAbs) as a potential target for HIV-1 vaccine development. They examined two longitudinal studies and the virus-antibody co-evolutionary pathways that resulted in cooperative bnAb lineages and suggest a possible recipe for HIV-1 immunogen design.[Abstract].
- From our undergraduate desk: Harvard student Kristen Rodrigues selected a paper from Eric Fischer's laboratory at Dana-Farber Cancer Institute that appeared in Cell in which the authors describe how the Human cGAS–DNA complex balances DNA length specificity with the magnitude of immune signaling response [More on Tumblr].
Software Changes
ATSAS version 2.8.4-1 was pushed out for Linux only. This version includes bug fixes and performance improvements along with 3 new programs: dammix, for restoring the shape of unknown component in an evolving system; pddffit, to fit a given pair distance distribution function to experimental data; and datft, for directing Fourier transform of experimental data to pseudo pair-distribution function.
CCP4 is now at version 7.0.060. This version includes a fix to the z-score output in molrep, a correction to LINK generation mode in acedrg, and in fragon, a custom fragment option in CCP4i2. Also included are updates to pointless, aimless, fragon, and rabdam.
crYOLO version 1.0.4 is new to SBGrid. crYOLO, from the Raunser Group and Thorsten Wagner at the Institute of Molecular Physiology, is a novel automated particle picking software based on the deep learning object detection system 'You Only Look Once' (YOLO).
DIALS was updated to version 1.10.3 and now has faster refinement for hierarchical multiple panel detectors by moving calculations to C++, a new option for scan-varying refinement of the goniometer setting matrix, an option to plot beam centre drift and error bars on scan-varying unit cell using dials.plot_scan_varying_crystal changed to dials.plot_scan_varying_model, improvements to profile fitting in the presence of negative-valued pixels, renaming of 'DQE' renamed to 'QE',improved support for Bruker Photon II detectors, a fix to dials.reindex when dealing with multi-sweep datasets, a fix to dials.refine_bravais_settings for multi-sweep datasets if experimental models differ between experiments, and one new program dials.cosym, which implements algorithms described in this publication: Gildea, R.J. & Winter, G. (2018). Acta Cryst. D74.
Gromacs version 2018.2 was pushed out.
HKL2000 version 717 is the first release with an automatic mode and uses the "Auto" tab to allow automatic indexing, integration, and scaling of data using the hkl_auto program. The automatic mode uses the CCP4 program "pointless" for final space group determination. Some formats or constructs supported in the manual mode are not yet available in the automatic mode. Other new features include new options to invert the beam position read from the frame header and a change to the 3D Window (the number of frames that will be processed together for indexing and integration) to calculate based on the frame width and memory limits of the denzo_3d program.
IGV was bumped to version 2.4.10. The 2.4 release includes support for PacBio long-read sequencing data and 10X Genomics sequencing data, a new alignment coloring option, support for CRAM files, and improvements to the interface for managing genomes.
Jalview is now at version 2.10.4b1 that includes critical patches for maintaining access to public web services and compatibility with Java 10 on OSX, along with several efficiency improvements, an improved 3D structure chooser and bug fixes to make SIFTS sequence-structure mappings more reliable.
PHENIX nightly 1.14-3211 is the latest version and available via version override.
PyMOL version 2.2 was pushed out. This version includes a unified modern user interface (PyQt replaces Tcl/Tk and MacPyMOL on all platforms), better third-party plugin and custom scripting support in the Anaconda Python distribution, MAE export with properties, and stereochemistry (”stereo”) labeling with RDKit or Schrodinger backend.
ROME System 1.1.0 is the newest addition to the SBGrid collection. ROME (Refinement and Optimization via Machine lEarning**) is a parallel computing software system dedicated for high-resolution cryo-EM structure determination and data analysis, which implements advanced machine learning approaches in modern
SAMtools version 1.8 has a number of bug fixes along with a few changes: samtools calmd now has a quiet mode enabled by passing -Q to calmd, a new option in samtools depth where -d 0 will effectively remove the depth limit, and improvements to collate's interface in SAMTOOLS, making it possible to specify an output file name using -o, instead of deriving it from the prefix used for temporary files.
Schrodinger's latest quarterly release - 2018-2 - was pushed out for those labs with access.
UltraScan III version 4.0 is now available. This version includes full integration of US-SOMO based on the same Qt5.x framework; support for the new timestate feature of the Optima AUC; support for fully threaded fitting applications with an unlimited amount of RAM, allowing desktop fitting to take advantage of large multi-core desktop computers; direct integration with the new Optima AUC instrument; rotor stretch calibrations support for the 7-channel calibration mask; many new interface improvements. Simplification of solution, buffer, and analyte databases, data editing, rotor stretch support in finite element simulations; integrated buffer tables (same as Sednterp), vbar and e280 from protein sequence, and absorbance spectrum support; new spectral fitter and decomposition tools; and new multiwavelength data analysis support functions.
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.