AmberTools23 update includes changes to forcefields with an OL21 update for DNA, an update to GAFF, and updated parameters for some post-translational modifications. The Quick package for Hartree-Fock and DFT electronic structure calculations is integrated into sander for QM/MM simulations along with significant performance improvements, a new geometry optimizer, and support for spin-unrestricted calculations. In cpptrj you'll notice GIST improvements, new cluster analysis, and a "prepareforleap" script with support for carbohydrates, and with the addition of fe-toolkit, users can analyze alchemical free energy calculations.
AreTomo2 1.1.2 corrects a mistake in generating the ordered list (csv file) for Relion subtomogram averaging. The first column of the csv file is now the chronological order in acquisition of tilt images. CTF estimation is also revised to improve robustness at high tilts. See Readme.txt for full details.
AutoDock-Vina 1.2.5 is a bug fix release. It fixes the sorting of output poses by energy.
CCP4 is now at release 8.0.017.
CCPNmr 3.2.0 has number of new features, including a dedicated Relaxation Analysis module, a new Chemical Shift Mapping Analysis module, auto and manual arrangement of peak labels, simulated 13C HSQC peak list, 1D strips, pinning for strips, Metabolomics module updates, and a new Bonds core object.
ColabFold 1.5.5 itegrates AlphaFold v2.3.1 with a new fine-tuned model from Deepmind for multimer modeling. All models can be used for either monomer or multimer prediction. bfloat16 is now enabled by default for both monomer and multimer models, the max number of recycles was increased from 3 to 20, the ability to subsample MSAs and enable dropouts is now available in the main notebook.
CryoSieve 1.2.3 is one of several new titles this month. CryoSieve is a tool for particle sorting/sieving in single particle analysis (SPA) for cryoEM.
DeepMainMast 20240112 is another new tool. DeepMainMast is a computational tool using deep learning to automatically build full protein complex structures from cryo-EM maps.
DIALS 3.18.0 includes an exclude_images_multiple= option to split a scan at calibration images in dials.slice_sequence, indexig.method=pink_indexer for still images in dials.index, and changes to dxtbx: a new XTC Format has a new parameter (spectrum_required=) to better handle spectra calibration for bad data, new Bruker and miniCBF format readers for the ELDICO ED-1 electron diffractometer with DECTRIS QUADRO detector, a FormatSMVTimePix_Su to always mask out the central cross of virtual pixels that have been reconstructed from wide edge pixels, and a new format reader for ISIS SXD detector.
DSSP 4.4 is a rewrite that offers full mmCIF support and now writes out an annotated mmCIF file by default, storing the secondary structure information in the _struct_conf category. DSSP also now defines Poly-Proline helices
Fragmenstein 1.0.2 is also new to the SBGrid collection. Fragmenstein merges, links and places compounds by stitching bound compounds together like a reanimated corpse.
mafft 7.52 is now available.
matchmaps 20240212 is new to SBGrid. matchmaps makes unbiased difference maps even for non-isomorphous inputs. The developers will introduce this title to SBGrid members during our July webinar.
Modeller 10.5 is a minor update that adds support for Python 3.12, improves the
mmCIF output, and adds initial support for new-style 12-character PDB IDs.
MotionCor3 1.1.1 incorporates changes of CTF estimation in AreTomo2 and fixes a number of bugs.
NABC 7bdc304 is another new title. NABC is molecular manipulation language, NAB (Nucleic Acid Builder), which interfaces to SFF (Simple Force Field) in Amber.
Probe 2.18.211005 is the new default.
PyMOL 3.0 is out and updates were to 2.6.0 LTS were applied as well.
PyRosetta M12024.10_arm is a version of PyRosetta for the M1 Mac.
Python 3.12.2 is now available.
qFit 2024.2 is another new addition. qFit is a collection of programs for modeling multi-conformer protein structures.
Reduce is now at version 4.14.
Relion-5 was updated to the latest beta, 5.0-beta2_cu11.8.
reliontomotools 1.0.0 is new. reliontomotools is a collection of tools for subtomogram analysis.
Rosetta 2023.45 was pushed out with support for Apple ARM CPUs.
Schrodinger 2024-1 is available. See the release notes for full details. This suite is available to non-profit labs in North America for an add-on fee.
SRA Toolkit 3.1.0 updates include an option to use prefetch --eliminate-quals to download SRA Lite data, vdb-validate to identify when data (blob) checksums are missing, new support for AlmaLinux
SSDraw 1.0 is the last of the new titles this month. SSDraw generates publication-quality protein secondary structure diagrams from three-dimensional protein structures with options to color by conservation score, B-factor, or custom scoring.
T-Coffee release 13.46 is available.
Uni-Dock 1.1.1 is the new default.
Vina-GPU 2.1 further accelerates AutoDock Vina and the most common derivatives with new docking algorithms (QuickVina 2 and QuickVina-W) with GPUs.
