BCFtools 1.19 allows users to filter expressions using a file with list of strings to match, query REF,ALT columns directly, along with many changes to specific commands.
Blast+ 2.15.0 allows users to limit searches using non-leaf taxID (e.g., all bacteria) without running a helper script, selects the best threading mode (i.e., sets -mt_mode option) based on your query and database for BLASTN, BLASTP, BLASTX, and TBLASTN, has an optimized batch size for blastx-fast for smaller databases, along with other performance improvements.
Bowtie 2 2.5.3 fixes a memory usage problem and crashes when processing empty FASTQ records, the problem of treating -f and -F as mutually exclusive, and adds new support for libsais to bowtie2-build for faster index building.
Choroma was added to SBGrid in January at version 20231201. Chroma is a generative model for designing proteins programmatically.
ChimeraX release 20230908 is available.
cisTEM 2.0.0 alpha is available via version override.
Coot versions 0.9.8.92 for Linux and 0.9.8.8 for Mac are now available.
cryoDRGN v3.1.0-beta includes a new interactive command-line interface known as cryodrgn_filter, an option to produce a plot of the learning curve in cryodrgn_analyze, an added cell in cryoDRGN_filtering jupyter notebook returned by cryodrgn_analyze for filtering by UMAP/PC values.
crYOLO 1.9.7 will be helpful for those who pick filaments in micrographs and tomograms, with optimization of the weight of the loss component responsible for estimating the filament direction and of default parameters when tracing filaments in 3D. There's also a fix to a bug that removed boxes at the end of each filament trace.
Dynamo-tools is new to SBGrid at version 1.0.0. Dynamo-tools is a collection of tools for subtomogram averaging in dynamo.
DIALS 3.17.0 is the new default and includes a number of improvements including the removal of circular dependencies between DIALS and cctbx.xfel by using the new serialtbx, a dials.import update to enable use of an image range selection when importing a still sequence, improved CC½ fitting in dials.estimate_resolution using a weighted tanh fit, an update to dials.find_spots and dials.integrate to accept exclude_images_multiple=N, a new dials.ssx_integrate command mosaicity_max_limit= setting to control the mosaicity limit considered unphysically large, a new max_cell_volume_change_fraction= parameter in dials.ssx_integrate to catch highly divergent cell refinements, a new dxtbx tool - nxmx_writer - for converting any data dxtbx can read to NeXus data, an update to enable slicing a subset of images/templates in xia2.ssx using <filename>:start:end syntax, in xia2.ssx_reduce improved workflow for resolving indexing ambiguity and a new starting_geometry= option to set an initial geometry for further geometry refinement, and in xia2.cluster_analysis, a run_cluster_identification= option to toggle cluster identification analysis
GROMACS release 2024-rc includes native use of the Colvars library, which simplifies the use of advanced enhanced sampling simulations, reduced artifacts from Lennard-Jones pair interactions on the pressure by a configurable increase of the Verlet buffer, and corrections to the deform option. Simulations with box deformation now behave correctly under high shear or when a solid or membrane fractures, a new option for hydrogen mass repartitioning in grompp enables easy access to performance improvements, AWH improvements include better control of the histogram growth factor and automatic scaling of the target distribution based on the AWH friction metric, and configurable HeFFTe multi-GPU FFT options let users fine-tune the settings.
IGV 2.17.0 changes include base modification options that now include the choice of monocolor and two-color schemes with colors for each modification and to represent the unmodified base. Alignment track updates include expanded insertions, redesigned so that insertions are now indicated with triangles under the genomic ruler, a new option to group by selected insertion locus, improvements to visualization of chimeric (split) reads, new graphical annotations for INDEL quality on SAM/BAM/CRAM files containing Ultima Genomics flow-based reads, and a new autosave feature for IGV sessions.
Isolde was added to ChimeraX versions 1.5 and 1.6.
MemBrain-Seg release e28baac is now available via version override.
ModelAngelo is now at release 1.0.12.
NMRPipe release 20230523 is the new default.
NAMD 33.0b5 is now available via version override. This update includes 3.0b5-universal-multicore for Mac and 3.0b5-multicore-CUDA /3.0b5-netlrts-smp-CUDA for Linux.
PEET 1.17.0 has an update to Matlab R0222b and added usePcaMotiveLists.
Phenix 1.21-5207 is the new default.
Protomo 3.1.0 includes subvolume 3D-alignment and classification (formerly called i3) and no longer depends on Python. This version also enhancements to scripts to align multiple tilt series in parallel.
relion_composite_masks is another new title. relion_composite_masks is a fork of relion 4.0.1 with support for multiple masks during refinement.
SCIPION 3.1.0 is now available.
Tomo3D 2.2 was pushed out.
TomoAND is now at version 2.0.
TomoTwin 0.8 is the new default. This version improves the user experience when working with the clustering workflow. You may notice that no label mask is created when calculating a umap because it is computed in the background.
Note: you will need to recalculate your umaps to take advantage of this change. Also new: a umaps progress bar, a time delay when selecting clusters in the umap between the selection and the actual highlighting, and automatic selection of an appropriate embedding file when saving cluster targets when possible.
XDSGUI 20230505 improvements include avoidance of strange characters in standard output upon reading images using the DECTRIS neggia library, an increase in the maximum length of file names to 256 now accepted by XDSCONV and XSCALE, and automatic removal of unused memory space in XSCALE.
