Newsletter

Dear Consortium Members and Affiliates,

Here in Boston the horizon always looks a little brighter when bidding farewell to February, but this year the warming weather and extra hours of daylight are especially welcome. As we wrap up the month, we've published a profile on SBGrid member Ho Leung Ng from Kansas State University, posted February webinars and fleshed out the March lineup, pushed out 9 software updates, and share a few technical notes on XQuartz, NFS issues, BigSur support, and beta testing for our new graphical installation manager. We also have 4 new members to welcome and 3 member publication highlights.    

This month's member Tale follows the journey of Ho Leung Ng to almost ever corner of the US, from his roots in Hawaii, to Massachusetts, then California, and finally to Kansas where his group at Kansas State University is working on a SARS-CoV-2 protease inhibitor and he founded the Open Source COVID-19 drug discovery consortium. [Read the full story]

We had a full month of software webinars in February, with presentations from Fabian Schoenfeld on GPU ISAC, Paul Emsley on Coot, and Yilai Li on CryoAssess along with a primer on SBGrid installation tools and the capsule environment from team members Jason Key and Carol Herre. We'll post the GPU ISAC webinar as soon as the authors publish data, but the other webinars are available on the SBGrid YouTube channel.

Note that SBGrid webinars are free and open to the public, so please feel free to share announcements or links with other who may benefit from these sessions.

A small software push went out this month, with updates to Coot, DIALS, Dynamo, EMAN2, IMOD, Modeller, MoRDa, PHENIX, and VMD. See Software Changes below for complete details.

Four new members joined in the month of February: David Hershey and Robert Landick joined a growing contingent from University of Wisconsin-Madison, Kamal Al Nasr is our first member from Tennessee State University, and Rectify Pharmaceuticals. Welcome to our newest members!

Technical notes from our Software Team

XQuartz: On macOS, many SBGrid-supported applications require XQuartz, and the recent series of XQuartz 2.8 beta update are not compatible with some applications. While the latest 2.8 rc1 update appears to fix these issues, we recommend waiting until there is a stable release before upgrading working systems. Remember that you must log out and log back in to use an upgraded XQuartz.

NFS issues on macOS: We are aware of a number of NFS problems on recent releases of macOS that appear to impact 10.15.7 and macOS 11. While we don't have in immediate solution to all these problems, the sbgrid-cli installation manager is available for users to install and use software locally on desktops and workstations. Register for an installation manager account at www.sbgrid.org/registration/register/.

macOS 11 Big Sur support: We've been testing new application installations on macOS 11 Big Sur. The majority of applications appear to work normally on both x86_64 and Apple Silicon hardware, with a few exceptions. If you have a new Big Sur M1 mac, you should be able to install software with the SBGrid installation manager. Be sure to install XQuartz, and let us know if you encounter any problems.

Installation Manager Beta Testing: Our new graphical Installation Manager for macOS and Linux is nearly ready to go and we are looking for some beta testers! Internal testing is going well and we would now like feedback from the community. Email bugs@sbgrid.org and we'll get you set up.
 

Community Announcements

Sonja Lorenz's Group, from Max Planck Institute for Biophysical Chemistry, has an opening for a Postdoc working on structural and functional analyses of ubiquitin ligase complexes.  The Lorenz laboratory aims to understand how ubiquitin achieves specificity in regulating virtually all aspects of eukaryotic cell biology. Full details here: https://www.mpibpc.mpg.de/17641630/04-21R

Member Publications

Over 125 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:

Deposit your experimental datasets:  If you're currently preparing a manuscript, please remember that, while you're making the PDB record deposit and publication submission, you can also preserve your primary experimental datasets with deposits to the SBGrid Data Bank.

Acknowledge SBGrid: SBGrid operations are funded with member fees and grants, and we are grateful when you acknowledge SBGrid in your presentations and publications.

Please use this SBGrid logo on your acknowledgements slide.

We also recommend the following boilerplate language for inclusion in publications that report results obtained using SBGrid supported software:

SBGrid citations:  SBGrid's eLife paper received 3 new citations in the month of February, from these SBGrid-member laboratories: Evripidis Gavathiotis from Albert Einstein College of Medicine in Nature Communications: Eltrombopag directly inhibits BAX and prevents cell death; Alan Brown of Harvard Medical School in Nature Communications: Structure of a microtubule-bound axonemal dynein; and Georgios Skiniotis and K. Christopher Garcia of Stanford University School of Medicine in Cell: Structural basis for IL-12 and IL-23 receptor sharing reveals a gateway for shaping actions on T versus NK cells.

Software Changes

COOT 0.9.4.1 is available. See the release notes for a list of changes, and be sure to watch our recent webinar featuring Paul Emsley talking about what's new in Coot. Watch here.

DIALS version 3.3.2 includes updates to dials.export, to allow export of data with either summation or profile fitted intensities, a fix to dials.scale when only summation intensities are present, performance improvements with internal mask generation, update dxtbx to fix miscounting of images in VDS nexus files and a cacheing bug with live per-image analysis of HDF5/SWMR files, and an update to the cctbx as_cif_block() method to match updated definitions of the pdbx mmcif v5 dictionary.

Dynamo was updated to version 1.1.514 (linux) / 1.1.511 (mac). See the version features section of the Downloads page for complete details.

EMAN2 version 2.9 is the first version based on Pyton3 and includes SPHIRE 1.4 and SPARX. Users will notice significant improvements to the tomography pipeline. Data compression is now a standard for both CryoEM and CryoET data processing pipelines, dramatically reducing disk usage and transfer times. This update also includes numerous improvements to in-situ subtomogram averaging with a full PPPT subtomogram averaging pipeline capable of near-atomic resolution, fully automated tilt-series alignment/ reconstruction with no need for fiducials, a dedicated deep-learning tomography particle picker, and simultaneous (visual) picking of multiple macromolecular species. You'll see extensive improvements to e2boxer, the deep learning picker and simple inline instructions. Also new are local resolution and filtration based on mFSC (Penczek), for SPA and SPT (iterative), new visualization options for volume stacks, support for EER format & oversampling, and better integration with Numpy and Jupyter.

IMOD updates to 4.11.2 and 4.11.3 were pushed with fixes to stop Subtomosetup from skipping some of the particles in each Z level, batch advanced option for solving for all tilt angles except one at minimum tilt,  Ctf3dsetup when using a temporary directory with a space in its full path, option not to fill gaps in Beadtrack, 2D Filtering in Etomo so file chooser, and Rawtiltcoords (used by Subtomosetup and Ctf3dsetup) for new style filenames.

Modeller 10.0 is a major update that adds support for residue numbers >= 10000 in PDB format files using hybrid-36 notation, assigns the chain ID 'A' to single-chain models to generate more standard PDB files, and uses CamelCase naming for all Python classes.

MoRDa 40 includes updates to the structure solution pipleline with a new feature for multimeric search models reduced to interacting domains, relevant for e.g.
solution of immunoglobulin structures. Also new is a command line option to use a search model missing from Morda database (e.g. a model that has not yet been deposited in the PDB). Users will also notice new command line options for tweaking MR trials with a
particular model, generated or provided by the user. Run morda_solve -h for details.

NMRPipe was updated to version 2021012PHENIX nightly build 1.19.1-4122 can be used with version override. This update fixes a bug in phenix.real_space_refine, restoring previous jobs, clarifying NCS options, improving rotamer fitting  and map/restraints weight calculation, and morphing can now use multiprocessing. In phenix.map_to_model and phenix.trace_and_build there is improved high-resolution model-building with detection of insertions and deletions. New methods include phenix.local_resolution to calculate a local resolution map and phenix.local_aniso_sharpen to optimize a map taking into account local resolution-dependence and anisotropy of the map and its errors. High-level scriptable Python tools are available for map and model analyses, manipulation, and for model-building.

Default restraints now adjust the "positions" of atom names is (pseudo-)symmetric amino acid side chains and improvements to ARG allow more flexibility of the CD atom.

VMD 1.9.4-alpha20201221 is now available via version override.
 

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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