BindCraft is new to SBGrid at version 1.2.0 BindCraft is a simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. Select your target, let the script do the rest of the work, and finish once you have enough designs to order.
Boltz-1 0.3.2 includes a small number of bug fixes.
CCP4 releases 9.0.004 and 9.0.005 were pushed out. 9.0.004 includes updates to many CCP4 applications including simbad, servalcat, and DIALS, as well as updates to the ccp4i and ccp4i2 GUIs. 9.0.005 includes updates for DIALS, xia2, and others. See https://www.ccp4.ac.uk/ccp4-8-0-updates/ for more info.
Chai-1 is another new title at version 0.5.2. Chai-1 is a multi-modal foundation model for molecular structure prediction and enables unified prediction of proteins, small molecules, DNA, RNA, glycosylations, and more.
ChimeraX 1.9 for macOS and Linux includes several new features. Session views are automatically saved, the sequence Region Browser now has a Details column for UniProt feature annotation, and most tools are now prohibited from docking into the top or bottom of the main window, in an effort to prevent the mayhem that results from accidentally docking a tool into the toolbar area. See https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog for more information.
cryoDRGN 3.4.3 introduces a new utility for making volume movies using model analysis results, along with some fixes and improvements to existing features.
Doppio is also new to SBGrid. Doppio is a web-based user interface for CCP-EM and RELION software. Release 1.1.0 includes numerous enhancements and bug fixes, including support for RELION 5’s Topaz, ModelAngelo, and class ranker by default.
GTalign 0.16.0-alpha is another new one. GTalign is a high-performance (HPC) protein structure alignment, superposition and search method (with flexible structure clustering ability). Both CPU and GPU versions are available with the ability to use multiple GPUs.
LipIDens 1.0 is a rebuild of the existing version 1.0. The new source fixes bugs in some download URLs.
napari-tomoslice is also new, at version 0.1.1. napari-tomoslice is a plugin for napari to aid in tomogram visualization and annotation.
OpenNucleome 1.3.0 is another new title. OpenNucleome is an open-source software designed for conducting molecular dynamics (MD) simulations of the human nucleus. It streamlines the process of setting up whole nucleus simulations through just a few lines of Python scripting and offers high-resolution structural and dynamic chromosome arrangements at a 100 KB resolution.
PDBImages 2.5.0 -- also new. PDBImages is a command-line tool from PDBe EMBL-EBI for generating images of macromolecular structures from mmCIF or binary CIF structure files based on Mol*.
ProteinMPNN 20250113 includes the new soluble model weights.
PyMOL 3.1.3 is now available and includes an update to python 3.10 and support for Schrodinger’s new license format. BCIF and GZSDF file support was also added. Additional changes can be found here: https://github.com/schrodinger/pymol-open-source/blob/master/ChangeLog
Python releases 3.6.0 and 3.6.15 were added for backwards compatibility with some user workflows.
R version 4.3.2 was also added to address backwards compatibility for some user workflows.
TEMPy-ReFF is the last of the new titles. TEMPy-ReFF is a flexible fitting and model refinement tool, using a Gaussian Mixture Modeling approach and gpu-accelerated molecular dynamics calculations. Developer tutorials can be found here: https://gitlab.com/topf-lab/tempy-reff-tutorials/.
Topaz releases 0.3.0 and 0.3.7 were pushed out. These latest versions contain a number of improved features, now allowing for larger training sets with mixed micrograph sizes and performance of particle extraction in patches. Topaz train now reports adjusted_precision, as a proportion of the theoretical max precision (pi), and can now read long argument lists using "@list_of_many_files.txt" in place of filenames or wildcards.
Schrodinger 2024-4 is the new default. This version includes numerous updates and bug fixes across the suite, including enhanced CryoEM surface performance in the Maestro interface. Notably, this release no longer supports the FlexLM License format., but uses Schrodinger’s new license manager. See https://www.schrodinger.com/life-science/download/release-notes/ for more information.
Warp 2.0.0dev31 is a minor update that includes a variety of bug fixes and updates.
