Dear Consortium Members and Affiliates,
For our October newsletter we'll open with the big news and our congratulations to the winners of the Nobel Prize in Chemistry! The rest can't really compete, but we still think you'll be interested in a major update to the SBGrid Data Bank, with a new user interface for depositing X-ray diffraction images, an upcoming EMAN2 webinar, a bit of background on James Fraser and his lab in UC San Francisco, a listing of position postings in member labs, a software push with 15 updates and one new title, new options to run SBGrid applications using Singularity, an updated version of the SBGrid Installation Client, three new members to welcome, and a couple of member publication highlights.
The Nobel spotlight is on CryoEM, with SBGrid-member Joachim Frank receiving the coveted award, alongside Jacques Dubochet and Richard Henderson, for his work developing the mathematical tools for image analysis that became SPIDER. This well-deserved recognition comes as universities invest in new microscopes and build out multi-million dollar facilities at a dizzying pace. We salute Dr. Frank and his colleagues and look forward to exploring and supporting this revolution in structural biology.
We would like to announce the launch of a new user interface for depositing X-ray diffraction images in the SBGrid Data Bankhttps://dataverse.sbgrid.org. This new interface offers additional functionality, including ORCID login integration and a new set of collaborative tools. To streamline the deposition process and assist you with new dataset uploads, SBGrid will offer a weekly office hour, on Tuesdays at 9AM EST - connect via zoom.us/j/6170001111.
EMAN2 is next on the roster of webinars. Steven Ludtke from Baylor College of Medicine will join us on Tuesday, November 14th with the latest EMAN2 news. Webinar details here. We also uploaded our October webinar featuring Toshio Moriya and a primer on the SPHIRE software package for cryo-EM single particle analysis to YouTube. Watch the SHIRE webinar.
We caught up with James Fraser at his University of California, San Francisco laboratory for our October member tale. Fraser clued us in on how baseball informs his approach to structural biology. Just as you can't know a player by statistics alone - you've got to see him in action - there is much to learn from the movement scientists can observe in structures as the temperature rises. Read the full story.
Don't forget to check out our listing of open positions in SBGrid member labs, and if you'd like to include a position posting for your lab, please email Michelle. [Job Postings Page].
We've pushed out lots of software updates during the last 30 days, including updates to ADXV, Anaconda, BioXTAS RAW, CCP4, CrystFEL, Gautomatch, Geneious, Grace, ImageMagick, Phenix, PyMOL, SBGrid install client GUI, Schrodinger, Xplor-NIH, and Pyrosetta, and one new software title: smina.
Run SBGrid anywhere with Singularity: We are now building applications and workflows into Singularity for use on High Performance Computing resources. Need an application or workflow for your favorite cluster? Want to us help test images? Let us know. More info on Singularity containers can be found here: http://singularity.lbl.gov.
The SBGrid installation clients have been updated with many new features and bug fixes. The latest version can be found at https://sbgrid.org/wiki/client_install.
Three new members joined SBGrid this month, two who are setting up new labs at Harvard Medical School - Alan Brown and Jonathan Abraham - and one new face from IBS Grenoble: Paul Schanda. 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 Structural Biology Data Grid 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.
Five new citations popped up for our SBGrid eLife paper this month. Thanks to all who remembered to include us: Mishtu Dey at U Iowa [Abstract]; Jean-Philippe Julien at U Toronto [Abstract]; Titus Boggon at Yale School of Medicine [Abstract]; Florian Schmitzberger [Abstract]; Brandt Eichman at Vanderbilt U [Abstract]; and two citations from Marc Kvansakul at La Trobe U [Abstract 1] and [Abstract 2].
We've still got a hiccup in code calling member citations from PubMed, so we can't give you the full listing, but we'd like to mention a couple of notable highlights:
- The "hinge" of the matter - in protein kinase conformational change. Showcased online this month in Biochimica et Biophysica Acta - Proteins and Proteomics is a new publication from Yale University School of Medicine's Titus Boggon revealing the atypical kinase conformational movements of PAK4 crystal structures.[Abstract].
- There are always exceptions to the rules & the anthrax bacteria seems to be one of them, at least in regards to Bacillus anthracis prolyl 4-hydroxylase & its affinity for collagen-like proline-rich peptides. Mishtu Dey's lab at the University of Iowa published a new paper in the journal Biochemistry focusing on the similarities of BaP4H to animal PHDs & collagen P4Hs as it acts on elongation factor Tu, suggesting promiscuous substrate recognition & a role in bacterial translation. [Abstract].
Software Changes
adxv is now at version 1.9.12.
Anaconda version 5.0.0 was pushed out with updates/additions to over 100 packages, including an update to MKL and the addition of JupyterLab alpha preview 0.27.0. New compliers for Mac and Linux improve security and performance. The developers use conda-forge as a base (using https://github.com/AnacondaRecipes) when possible. You'll also notice a new pkgs/main channel that is given top priority within defaults and holds packages built with the new compiler stack.
BioXTAS RAW version 1.3.0 has some new major features including, similarity testing for scattering profiles using the CorMap test, which is done automatically when averaging profiles or picking a buffer region of a SEC curve. You'll also notice that absolute scaling can now be done using the NIST glassy carbon standard SRM 3600, there is a new option for normalized Kratky plots in the right click menu and a results summary panel for dammif/n reconstructions that shows the NSD, resolution (if SASRES is installed), and statistics about the individual reconstructions including chi squared, rg, dmax, excluded volume, and molecular weight.
CCP4 version 7.0.45 includes a bunch of bug fixes.
CrystFEL version 0.6.3 includes support for CBF files as input, the addition of the TakeTwo indexing algorithm, improved peak detection and basic hitfinder functionality, and new support for 3D detector geometry with detector panels that are not perpendicular to X-ray beam and "rail direction" can be specified.
Gautomatch version 0.56 fixes rectangle micrograph bugs and adds three new options: --detect_ice --T_norm_type --do_bandpass. These options offer more advanced control for better picking.
Geneious version 11.02 was pushed out. New features include options to annotate potential restriction sites that can be introduced by silent mutations and visualize gene expression in an interactive view that synchronizes your selection with the Annotations and Sequence View. CRISPR improvements include new support for the Cpf1 enzyme variant with 5' PAM site and a 'Target Sequnce' qualifier. Fastq import is better, now that paired reads can be associated with each other during import, and users can now set read technology during import.
Grace version 5.1.25(_2) is now available.
Imagemagick was updated to version 7.0.7-5.
Phenix nightly build dev-2875 is now available and fixes a couple of bugs in the phenix.real_space_refine GUI: 1) secondary structure restraints are not always enabled and 2) updated the file input interface to be similar to phenix.refine GUI.
PyMOL is now at version 2.0.2, and with the jump up to version 2 has introduced some major changes including a unified modern interface - the PyQt interface replaces Tcl/Tk and MacPyMOL on all platforms; better third-party plugin and custom scripting support with the Anaconda Python distribution, and open access incentive executables with a new licensing mechanism.
SBGrid install client GUI was updated to version 1.0.642. For those of you using this tool to manage your installations, the biggest improvement is a new search feature along with a bevy of bug fixes. The latest version can be found at https://sbgrid.org/wiki/client_install.
Schrodinger third quarter update 2017-3 is the new default.
Xplor-NIH version 2.46 is out and users may notice that, in eginput/psl/, there is a new example of the progressive stereo locking (PSL) algorithm for determining the chirality of natural products and other small molecules using primarily RDCs.
PyRosetta is now at version 4-115.
smina version 20170429 is new to SBGrid. Smina is a fork of AutoDock Vina customized to better support scoring function development and high-performance energy minimization.
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.