Newsletter

Dear Consortium Members and Affiliates,

September has arrived to usher out summer so the academic season can take its turn to heat up. We're falling in line with the return of our weekly webinar series, 4 new members to welcome, 3 publication highlights, and the latest round of software updates and new titles.

After a brief hiatus, we'll restart our webinar series in mid-September, kicking things off with scientific talks from the laboratories of Daniel Minor, Jason McLellan, and Qing Fan. See the September dates below, or check our website  for the full listing. If you're new to SBGrid, be sure to visit us on YouTube - SBGridTV - to see our full collection of past presentations from structural biologists and software developers.

We've got a big software push this month, with updates to 17 titles - ACEMD, BioXtas RAW, CCPEM, Cryofit2, crYOLO, CTFFIND4, DIALS,  ISOLDE, MAFFT, MoRDa, NAMD, Phenix, PLUMED, pyEM, PyMOL, RELION, and Schrodinger  - and 3 new applications:  ALEPH, CryoAssess, and TVIPS Tools. See Software Changes below for complete details.

August brought four new members, with Jamaine Davis our first member from Meharry Medical College, Vanessa Ruta becoming our seventh lab at Rockefeller University, Catherine Day joining a growing contingent in New Zealand at the University of Otago, and Andres Kaech joining as the eighth member at University of Zurich. Welcome to our newest members!

Technical notes from our Software Team

Linux users should note that the PATH length bug in CentOS7 persists in CentOS8.

Community Announcements

New position postings came through from these three SBGrid members this month.

Cryo-EM Specialist at Harvard Cryo-EM Center for Structural Biology. Harvard Medical School houses two core facilities providing access to negative stain and cryo-EM instrumentation; we are looking for a highly motivated scientist to join our team. The

Harvard Cryo-EM Center for Structural Biology, formed as a consortium between HMS, Boston Children's Hospital, Dana-Farber Cancer Institute, and Massachusetts General Hospital, serves the consortium members and a variety of external academic and commercial users. The Molecular Electron Microscopy Suite is a training resource for Quad-based researchers at Harvard Medical School. The successful candidate will provide support and training for researchers seeking to learn cryo-EM and negative-stain EM in these two facilities, serving as an interface between the instrumentation and a vibrant scientific community. The candidate will work closely with a team of scientists to support COVID-19 and related projects in many research areas and will take on facility management responsibilities.

The Protein Engineering group within Sanofi's Large Molecule Research Department is seeking a highly talented Computational Scientist for a postdoctoral position to focus on developing a machine learning approach to predict epitope-paratope, given any antibody-antigen pair, by combining an in-depth understanding of structure biology, antibody engineering, and large datasets both internally and externally.

The Deaconescu Lab at Brown University has one opening for a postdoctoral researcher. The laboratory's interests lie primarily in stress responses, with particular emphasis on responses to DNA damage and the mechanochemistry of DNA-based motors. We utilize a combination of biochemical, biophysical and structural techniques (e.g. X-ray crystallography, small-angle X-ray scattering, transmission electron microscopy).

For additional details on these SBGrid member position postings, see our website.

Member Publications

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:

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:

SBGrid's eLife paper received 4 new citations in the month of August from these SBGrid-member laboratories: Jason McLellan's group at University of Texas at Austin in PLOS Pathogens: Recognition of a highly conserved glycoprotein B epitope by a bivalent antibody neutralizing HCMV at a post-attachment step; Peter Mace and Catherine Day from University of Otago in PNAS: A cryptic tubulin-binding domain links MEKK1 to curved tubulin protomers; John Kuriyan and Eva Nogales of University of California, Berkeley in Nature: Structural basis for dimerization quality control; and James Letts from University of California, Davis in eLife:  Atomic structure of a mitochondrial complex I intermediate from vascular plants.

Software Changes

ACEMD version 3.3 includes an update to the latest OpenMM version, an improvement to the PRMTOP file parser, and integration of PLUMED, to bring state-of-the-art free energy calculation capabilities to ACEMD. Check the ACEMD documentation page for more details.

ALEPH is new to SBGrid at version 1.2.7. ALEPH is a bioinformatics tool to generate customized fold libraries for fragment-based molecular replacement. It provides several algorithms to interpret and analyze protein structures.

BioXtas RAW 2.0.3 introduces a major new feature with a new RAW API, allowing users to call RAW functions in their own scripts.

CCPEM has a new nightly release, version 20200722, that is available via version override.

CryoAssess 0.1.0 is new to SBGrid. CryoAssess is an automatic pipeline for cryo-EM data preprocessing and assessment using a combination of deep learning and image analysis tools.

Cryofit2 - Phenix was updated to include Cryo_fit, for fitting to a Cryo-EM Map using Phenix’s Molecular Dynamics.

crYOLO version 1.7.5 includes a fix so that training works when no filter is used, an improvement to the config file value max_box_per_image to automatically adapt to the given training data, fixes a bug that caused crYOLO to crash when no particles were picked, and fixes network architectures “crYOLO” and “YOLO”.

CTFFIND 4 version 4.1.14 is primarily a bug fix release.

DIALS version 3.1.0 has a number of improvements including a new command to identify connected regions of missing reflections in the asymmetric unit, new options and modes for image stacking in dials.image_viewer, dials.scale now separates anomalous pairs during error model analysis, a new parameter to optionally use pedestal-and-gain corrected data, and a new option in dials.combine_experiments to reject experiments with too many reflections

ISOLDE 1.0 is out with big changes in support for models with residues that the MD engine doesn't recognize using a new unparameterized residues tool to find all unmatched residues and suggest the most likely matching MD templates. A new "isolde add ligand" command will add any known ligand from the Chemical Components Dictionary and "isolde add water" adds a water molecule. The "isolde replace ligand" command, which is somewhat experimental, will turn one ligand into a related one, keeping and renaming all atoms they have in common. You'll also notice improvements to the ISOLDE menu, with new tools toform/break disulphide, add/remove a bond, etc. In response to many requests, a new "isolde step" command makes it much easier to systematically work residue-by-residue through your model.

MAFFT is now at version 7.471. See a complete list of updates in this changelog.

MoRDa version 33 is now available.

NAMD 2.14 updates were pushed for Linux to include multicore, cuda, netlrts, and netlrts-cuda, and for mac multicore and netlrts versions.

PLUMED 2.6.1 is the new default. With this upgrade PLUMED input file parsing is now case insensitive (uppercase compatible with former versions), partial_tempering now uses gawk instead of awk, Asmjit is now embedded into PLUMED (configure with --enable-asmjit), added a new --idlp4 option to driver to read DLPOLY4 HISTORY files, added atom selectors using mdtraj/MDAnalysis/VMD syntax, in includes new shortcuts (@sidechain-#, @back-# ) for selecting protein atoms, has the new models Maze and ANN.

pyEM is now at version 20200813.

PyMOL 2.4 has a unified modern user interface with the PyQt interface replacing Tcl/Tk and MacPyMOL on all platforms. It also includes an Anaconda Python distribution, better third-party plugin and custom scripting support, and open access incentive executables.

RELION 3.1.0 is the new default and includes high-order aberration correction & anisotropic magnification correction in CTF refinement, an external jobtype to run third-party software in the RELION pipeline, schedules for designing & executing on-the-fly processing procedures, and tweaks to the GUI, pipeliner, and helical processing. Support for the EER movie format is not yet available.

Schrodinger release 2020-3 is the new default.

TVIPS Tools 0.0.3 is another new SBGrid title.  TVIPS Tools is used to convert microED data collected on TVIPS TemCam-F416, Thermo Fisher CetaD, and Thermo Fisher Falcon III to SMV crystallographic format (*.img).

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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