AMBER version 24 represents a significant update from version 22, which was released in April 2022. The Amber24 package builds on AmberTools24 by adding the pmemd program, which resembles the sander (molecular dynamics) code in AmberTools, but provides (much) better performance on multiple CPUs, and dramatic speed improvements on GPUs.
BCFtools 1.21 includes changes to eleven subcommands as well as several overall changes.
CCP4 release 9.0.003 is a major update that includes COOT 1.10 and Moorhen for model building and refinement. This release also includes updates to servalcat and arcimboldo and a bug fix for jscofe.
ChimearX version 1.8 includes support for reading predicted aligned error (PAE) data from AlphaFold 3, reading docking results from MOE, fetching atomic structures and maps from PDB-REDO, and fetching/display of PDB NMR-STAR restraints. Users can now show worm depictions of attribute values and attribute values with atomic radii using the Render by Attribute tool, show multiple alternate locations simultaneously with "altlocs show", use "pbond" to create arbitrary pseudobonds and "measure contactarea" to report the area of one surface within a cutoff distance of another, and use segmentations tool for any volume data.
ColabDesign 1.1.2 introduces significant updates to its protein design tools, including improvements to PLDDT and PAE loss calculations, MLM support, and the addition of solubleMPNN weights.
CombFold 20240311 is a new SBGrid title. CombFold is a pipeline that predicts the structure of large protein complexes starting from the sequences of chains in the complex, accommodating up to 18,000 amino acids and 32 subunits. It utilizes AlphaFold-Multimer (AFM) to predict structures of "possible subcomplexes," which are combinations of subunits from the target complex. The CombFold Combinatorial Assembly algorithm then assembles these predicted subcomplex structures into a single large complex.
Fourier3D version 72a9edf is new to the collection. Fourier3D is a C++ based command line utility for tomogram binning, offering tunable flags and support for large tomograms through the use of intermediate data files, which can be written to disk during processing.
Glow 2.0 is another new title. Glow is a versatile markdown tool offering both a text-based user interface (TUI) for interactive browsing and a command-line interface (CLI) for direct manipulation of markdown content.
GPHL 2024 introduces new tools for wavelength error analysis, improvements to HDF5 dataset handling, support for partial charges in BUSTER refinement, a new tool (aP_fit_wvl_to_spots) for analyzing wavelength errors in processed datasets, improved handling of HDF5 datasets and meta-data extraction, support for partial charges in BUSTER refinement, improved TLS information extraction from mmCIF files (cif2tls tool), and updates to Grade2 for CSD-core configuration and in-house database support
MDAnalysis 2.7.0 introduces support for Python 3.12, a new GROMOS11 Reader, and chainID improvements, alongside various enhancements and deprecations in preparation for version 3.0.
Olex2 1.5 contains a reworked help system and two new tools: NoSpherA2 and EXTI.
ORCA 6.0.0 is a major release with extensive changes, improvements and speed enhancements. Note that ORCA is not included by default and is only available to academic and non-profit labs after registration.
Protkit 0.3.0 is new to SBGrid. Protkit is a Python library for structural bioinformatics, protein engineering, and machine learning. It offers tools for file handling, database access, protein representation, structure analysis, property calculation, and geometric operations.
pyRMSD is new to SBGrid at version 4.3.2. pyRMSD is a Python-based CLI utility that offers pairwise RMSD calculations on protein conformation ensembles with multiple algorithm choices
pytom-match-pick is new to SBGrid at version 0.7.2. pytom-match-pick is a GPU accelerated python module that significantly improves speed and sensitivity when using template matching to detect macromolecules from tomograms. It is available as a standalone module or for use from within PyTOM.
RELION was updated to 5.0-beta3_cu11.8_20240827. This new version fixes a bug that caused RELION to fail to write output from tomogram particle picking.
RingMapper 1.2 is new to SBGrid. RingMapper performs RING-MaP and PAIR-MaP analysis (RingMapper & PairMapper).
SAMtools 1.21 is the last SAMtools / HTSlib release with CRAM 3.0 as the default CRAM version. Going forward the default will be CRAM 3.1, unless the version is explicitly specified, for example using samtools view -O cram,version=3.0. This release includes numerous other new features and bug fixes.
TOMOMAN 0.9_20240919 is a minor bug fix update and is the new SBGrid default.
Udock2 20240909 is new to SBGrid. Udock2 is an interactive multi-body protein-protein docking software that predicts the geometry of protein interactions through an intuitive real-time docking procedure with on-the-fly scoring.
Warp 2.0.0dev27 and 2.0.0dev28 are now available.
XDS 20240723 has major changes including some data format changes, speed enhancements, and inclusion of two new utility programs: GECORR and REZEL. Notably, this version uses a new method for estimating the background in each image pixel in the COLSPOT and INTEGRATE steps of XDS.
