Dear Consortium Members and Affiliates,
We have a short update from the SBGrid team as we close out the summer, with an alert from our software team to upgrade to the newest version of our installation manager (see technical notes for details), a starting lineup for our webinar series, 7 software updates and 1 new title, 3 new members to welcome, and 3 member publication highlights.
Our webinar series will restart at the end of September and we'll kick things off on September 28 with an update from Alessandra Villa on GROMACS. If you would like to learn more about a particular software title or have a story from your lab that you'd like to share, please contact Michelle at email@example.com.
Our August software push includes updates to CrystFEL, DENSS, DIALS, MoRDa, OpenMM, ORCA, and Schrodinger along with one new title: dynamo2m.
See Software Changes below for complete details.
We had three new members join in the month of August: Wei Zhang from the University of Minnesota, Bo Liang from Emory University, and Tao Che from Washington University, St. Louis. Welcome to our newest members!
Technical notes from our Software Team
End of life for older version of the SBGrid installation manager
SBGrid Installation Manger downloads: https://sbgrid.org//wiki/client_downloads
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:
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, so we are grateful when you are able to acknowledge SBGrid in your presentations and publications.
Please use this SBGrid logo on the acknowledgements slide of your presentations.
We recommend the following boilerplate language for inclusion in publications that report results obtained with SBGrid supported software:
SBGrid citations: SBGrid's eLife paper received 3 new citations in the month of August, from these SBGrid-member laboratories: Cristina Paulino and Dirk Slotboom of University of Groningen in PNAS: Insights into the bilayer-mediated toppling mechanism of a folate-specific ECF transporter by cryo-EM; Eric Fischer from Dana-Farber Cancer Institute in Molecular Cell: Solenoid architecture of HUWE1 contributes to ligase activity and substrate recognition; and Alexandre Bonvin from Utrecht University in Journal of Chemical Information and Modeling: Shape-Restrained Modeling of Protein–Small-Molecule Complexes with High Ambiguity Driven DOCKing.
CrystFEL version 0.10.0 sports a new graphical user interface, support for electron diffraction, temporary removal of geoptimiser and pink beam support, improved MTZ and XDS output, improved options for bad pixel masking, and significant improvements in speed.
DENSS was updated to the latest version, which includes an option to enforce dihedral symmetry. See the news page for more information on this and other recent changes.
DIALS 3.6.0 has several new features, including dials.reference_profile_viewer, a new program for viewing reference profiles dumped by dials.integrate, along with updates to dials.combine_experiments with unindexed reflections in the combined output,
dials.image_viewer with improvements to overlays, basis vector control, and automatic color choices, and dials.reciprocal_lattice_viewer now displaying the "nearest point" and the default marker size scales based on intensity. Users may also notice a new module in dxtbx - dxtbx.flumpy - for zero-copy conversions between numpy and scitbx.array_family.flex arrays, and that setting absorption_level= parameter will ensure that absorption correction is always enabled in dials.scale and that option share.absorption=True allows shared absorption correction between sweeps when using the physical model. One note: future releases will require Python 3.7 or later.
dynamo2m 0.2.2 is new to SBGrid. dynoamo2m is a small set of tools providing a bidirectional interface between the subtomogram averaging software Dynamo and the Warp-RELION-M pipeline.
MoRDa release 42 was pushed out with new options in the structure solution pipeline: multimeric search models reduced to interacting domains, a command line option to use a search model missing from Morda database, and new command line options for tweaking MR trials with a particular model.
OpenMM 7.5.1 is a patch release that includes preliminary (beta) support for ARM-based Macs.
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.
This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium, the Structural Biology Grid computing consortium.
More information about the SBGrid Consortium is available at https://sbgrid.org
Report software bugs: sbgrid.org/bugs