Dear Consortium Members and Affiliates,
October news from the SBGrid Team includes a TomoTwin-cryoet webinar on Nov 8th, a software push with 8 updates and 4 new titles, 2 new members to welcome, some technical notes on the new MacOS, new size recommendations for the full SBGrid software collection, and RELION release notes, and 3 member publication highlights.
Next up for our software webinar series, join us on November 8th to hear from Thorsten Wagner on a brand new tool: TomoTwin-cryoet, for particle picking in Tomograms using triplet networks and metric learning. Register here for the series. Many thanks to Jan Koskinski for kicking off the series in October with a primer on Assembline. The video for that talk will be up on the SBGrid YouTube channel by the end of the week.
AreTomo was updated to version 1.3
Avogadro was updated to release 1.2.0 for the default, and 1.9.7 is available via version override as the latest Beta for Avogadro 2.0.
CCP4 8.0.005 is now available via version override.
COOT was bumped a couple of releases to 0.9.8.5 and includes updates to include the AlphaFold pLDDT colour scheme, ignore carbonyl oxygens in merge fragments, allow refinement of inter-chain links, and re-enable the picking of hydrogen atoms in rotation/translation.
IDPConformerGenerator 0.6.15 is new to SBGrid. IDPConformerGenerator is a modular platform for generating ensembles of disordered protein states that builds conformers by sampling backbone torsion angles of relevant sequence fragments extracted from protein structures in the RCSB Protein Data Bank.
ISOLDE 1.4 was updated for compatibility with ChimeraX 1.4. The GUI was completely revamped and rebuilt for more consistency and usability. The most-used controls are now in the top ChimeraX ribbon menu.
ModelAngelo is new to SBGrid at version 0.0.1. The latest tool from the laboratory of Sjors Scheres, ModelAngelo is an automatic atomic model building program for cryo-EM maps. It works best when users have access to GPUs with at least 8GB of memory. Mark your calendar for March 14th, when Kiarash Jamali introduce ModelAngelo as part of our webinar series.
Paramagpy 1.2 is also new. Paramagpy is a python module for calculating paramagnetic effects in NMR spectra of proteins and includes fitting of paramagnetic susceptibility tensors to experimental data associated with pseudocontact shifts (PCS) residual dipolar couplings (RDC), paramagnetic relaxation enhancements (PRE) and cross-correlated relaxation (CCR). It also has a GUI for easy viewing of data and a seamless transition between PCS/RDC/PRE/CCR calculations.
RELION 4.0 is out, with a new approach to subtomogram averaging with better weighting of the individual 2D images that make up a tilt series in relion_refine implementation of single-particle concepts of Bayesian polishing and CTF refinement for tomography data. Also new is a Variable-metric Gradient Descent with Adaptive Moments (VDAM) refinement algorithm for faster 2D and 3D classification, automated 2D class selection, a framework for automated execution of predefined workflows, and tighter integration of the pipeliner with CCP-EM software
SCIPION release 3.0.12 is out and available via version override. Note: due to its large size this software is available for inclusion by request.
topaz-filament 20220325 is a new fork of Topaz for helical filament picking.
Xmipp was updated to 3.22.07.
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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