ATSAS 3.2

What's new in ATSAS 3.2.1

Supported Platforms:
  • Linux (Ubuntu-20.04/22.04, OracleLinux 8)
  • MacOS (11.X Big Sur, 12.X Monterey, 13.X Ventura, all: x86_64 only)
  • Windows 10 and 11
Changes in Programs:
  • mmCIF support:
    • improved element lookup by ATOM name and residue type
  • chromixs:
    • fixed range selection by mouse
  • damaver:
    • if multiple models exist in an input file, use the first model, not the model with the id '1'
  • dammin:
    • make sure that a dummy atom radius is present for start volumes
    • correctly error out if the start volume could not be read
  • primus:
    • fixed range selection by mouse
  • ranch:
    • fixed assignment error if HETATM coordinates come first in a domain
  • sasref:
    • if multiple models exist in an input file, use the first model, not the model with the id '1'

What's new in ATSAS 3.2

Supported Platforms:
  • Linux (CentOS-7/8, Debian-11, Ubuntu-20.04/22.04)
  • MacOS (11.X Big Sur, 12.X Monterey, 13.X Ventura)
  • Windows 10
Removed Programs:
  • datadjust: use 'datmerge --scale --constant' instead
  • saspy: the Tk based plugin is outdated
Changes in Programs:
  • all:
    • PDB parser: reject invalid coordinates
    • PDB writer: add REMARK section on PDB output
  • ambimeter:
    • write files in mmCIF format
    • performance improvements
  • beadwaxs:
    • read/write files in PDB and mmCIF format
  • bunch:
    • read/write files in PDB and mmCIF format
  • coral:
    • read/write files in PDB and mmCIF format
    • mark residues in termini and linker as UNK
    • error out if there is no rigid body
    • fixed a crash on error exit
  • damaver:
    • avoid crash on exactly two inputs
    • warn about failed FSC calculations
  • dammin:
    • fixed an issue with input intensities of exactly zero
    • fixed an issue with possibly incorrect penalties with P2 symmetry and direction of anisometry
  • datmerge:
    • use global minimization to take all data into account
    • regrid data to internal low-density grid if not on same angular vector, scale and merge original data; use datcombine to provide a target grid
    • renamed option 'factors' to 'coefficients'
    • added option 'constant' to allow for 'adjust' operation on multiple inputs
    • added option 'scale' (data is merged without scaling or constant adjustment by default)
  • elllip:
    • read/write files in PDB and mmCIF format
  • flexbin:
    • read/write files in PDB and mmCIF format
  • gasbori/gasborp/gasbormx:
    • read/write files in PDB and mmCIF format
    • use biopolymers.cif for amino acid form factors
    • fixed an issue with possibly incorrect penalties with P2 symmetry and direction of anisometry
  • globsymm:
    • read/write files in PDB and mmCIF format
  • glycosylation:
    • read/write files in PDB and mmCIF format
    • use glycosylation_database.cif instead of internal binary data for data lookup
    • output of glycans as HETATM
    • fixed residue sequence numbering
  • pre_bunch:
    • use biopolymers.cif instead of internal binary data for data lookup
  • primus/qt:
    • added wizard for ambimeter
    • added wizard for datcombine
    • added wizard for shanum
    • added wizard for batch data conversion to absolute scale
    • added batch processing to regrid wizard
    • use datmerge with all-data global minimization for scale and adjust operations
    • added an (optional) column to manually enter a background constant
    • wizards accept files in mmCIF format where the corresponding application accepts it
    • added configurable and mouse-movable markers (text, symbol, lines) to plots
    • keep (more) lists of recently used files
    • fixed display of multiple properties with the same key, e.g. 'parents'
    • improved error message if the form-factor file for 'arbitrary polydisperse' is missing
    • improved layout and scaling on 2K/4K monitors on Windows
    • migrated to Qt-6.2
  • ranch:
    • use biopolymers.cif instead of internal binary data for data lookup
  • sasref/sasrefcv/sasrefmx:
    • read/write files in PDB and mmCIF format
    • improved chain assignments when writing models
    • performance improvements
    • fixed a double-allocation issue when working with neutron data
  • seqstat:
    • use biopolymers.cif instead of internal binary data for data lookup
  • sreflex:
    • read files in PDB and mmCIF format
    • fixed lookup of companion binaries on Windows

What's new in ATSAS 3.1.3

Supported Platforms:
  • Linux (CentOS-7/8, Debian-10/11, Ubuntu-18.04/20.04/22.04)
  • MacOS (11.X Big Sur 12.X Monterey)
  • Windows 10
Changes in Programs:
  • crysol: fixed an error that lead to program crash with higher harmonics (--lm=XX)

What's new in ATSAS 3.1.2

Changes in Programs:
  • all:
    • improved error handling when reading mmCIF,
    • improved heuristic to guess element from atom name when element column is missing.
  • chromixs: use ATSAS icon theme;
  • crysol: set the correct structure filename in .alm files (e.g. for sasref);
  • damaver: correctly report the best score;
  • elllip: Fixed a potential issue where non-equal length lipids could be truncated;
  • gajoe: fixed a wrong label in an output file;
  • primus/qt: show properties with duplicate keys, e.g. parents;
  • sreflex: do not set a unit for crysol by default, and only forward units if defined at the command line;

What's new in ATSAS 3.1.1

Changes in Programs:
  • cifsup:
    • do not convert atomic models to dummy models on output,
    • NCC: error out if crysol failed to calculate intensities;
  • coral: error out if crysol failed to calculate intensities;
  • crysol:
    • do not exit after warning on missing errors,
    • enforce smax of 2.0 Å-1,
    • when calculating the Slope of the net intensity, use a longer range than the first two points only,
    • default units are undefined, try to guess whether units are 1 or 2,
    • added unit types 3 and 4;
  • damaver:
    • fixed an issue with clustering where too few clusters would be identified,
    • write out superpositioned models by group,
    • write FSC and resolution estimate to prefix-fsc.dat;
  • dammin: fixed calculation of phase volume in output file;
  • ffmaker: when calculating the Slope of the net intensity in pool mode, use a longer range than the first two points only;
  • gajoe: limit maximum value for --minimum option to 50;
  • glycosylation: updated the internal database to modern PDB/mmCIF conventions, renamed residues and atoms;
  • gasbormx: added the general output filename prefix to monomer.dat and oligomer.dat;
  • monsa: fixed monsa phase filtering in output and fixed calculation of phase volume in output file;
  • ranch:
    • fixed an issue with domain assignments on different chains,
    • verify that residue sequence numbers are positive,
    • verify that there are random components that can be generated;
  • sasrefcv/sasrefmx: error out if crysol failed to calculate intensities;
  • sasres: removed all options related to alignment, now calculates FSC and resolution of pre-aligned models only (cifsup/damaver/3rd party software);
  • all:
    • avoid recognising HETATM as dummy residues,
    • do not use atom name 'C1' to identify the nucleic acid backbone, use 'P' as previously.

What's new in ATSAS 3.1.0

New Programs:
  • cifop: linear transformations of atomic and dummy atom models;
  • cifsup: superposition of atomic structures and dummy atom models with multithreading support;
  • datcombine: aggregation of data from multiple instruments;
  • nnlsjoe (EOM): alternative implementation of gajoe using non-negative least squares.
General Changes:
  • added MINPACK for numeric minimization;
  • added QUADPACK for numeric integration;
  • where possible, use BLAS/LAPACK algorithms, especially least squares and SVD; implementation on Windows and Linux by Intel Math Kernel Libraries (MKL), Performance Libraries on MacOS (related changes to individual applications not listed);
  • libatsas.{dll,dylib,so} is now a shared resource between all binaries, procedures are made ready for multi-threading;
  • open data sources: some internal data sources have been exported to .cif database files stored in $ATSAS/share that are parsed by applications on startup; may potentially be modified/updated/amended by users.
Changes in Programs:
  • beadwaxs: added penalties for non-uniformity and border beads with high contrast;
  • bodies:
    • use QUADPACK numerical integration for improved precision and performance,
    • use MINPACK for minimization,
    • added a search volume mode to generate start models for dammin and monsa, also provides a DAMSTART model in Fit mode,
    • write output models in DAM and Search Volume mode in PDB or mmCIF format,
    • added membrane protein body types;
  • cifop: added regrid option to allow conversion of atomic to bead models;
  • coral: use updated library implementation of crysol;
  • crysol:
    • use Chemical Components Dictionary (components.cif) to determine implicit hydrogens,
    • use ASAXS related form-factor data from .cif database,
    • use individual form factors for dummy residues,
    • recognise dummy atom models and calculate scattering appropriately,
    • implements directional and dummy-water shell,
    • support for mmCIF input file format,
    • removed re-binnning of experimental data to make chi-square values of fit comparable,
    • removed calculation and output of envelope (.flm),
    • NEW: Python bindings for crysol;
  • cryson:
    • added exchangable explicit H/D,
    • removed calculation and output of envelope (.flm);
  • damaver:
    • integrated all of damsel, damsup, damaver, damfilt, damclust,
    • employ any of the methods implemented in cifsup;
  • dammif: write output DAM in mmCIF format;
  • dammin:
    • write output DAM in mmCIF format,
    • read start model in mmCIF format;
  • dammix:
    • write output DAM in mmCIF format,
    • use updated library implementation of crysol;
  • datregrid: replaced option --template with --template-copy and --template-avrg;
  • em2dam:
    • write output DAM in mmCIF format,
    • use updated library implementation of crysol to calculate scattering;
  • ffmaker:
    • use updated library implementation of crysol, updated crysol options,
    • support for mmCIF input file format,
    • multitthreading support for many input files,
    • pool mode to calculate size distribution, e.g. of ranch models;
  • gajoe (EOM):
    • removed intensity and pool calculation, use ffmaker --pool instead,
    • performance improvements;
  • monsa:
    • write output DAM in mmCIF format,
    • read start model in mmCIF format,
    • improved stability of reading of master file, improved error reporting,
    • performance improvements;
  • nmator:
    • use updated library implementation of crysol, added crysol options,
    • support for mmCIF input file format;
  • primus/qt:
    • added alternative view to distribution of residuals (should be Standard Normal),
    • added alternative view to distribution of chi-square values when comparing many data sets pairwise,
    • ab initio wizard now accepts an .out file to work with,
    • added wizards to calculate theoretical SAXS/SANS with crysol/cryson without fitting,
    • added/updated hybrid modelling wizards for crysol/cryson/nmator/sreflex,
    • ribbon-style tabbed toolbar with large icons,
    • added "Open Recent" for all wizards that require files,
    • new icon theme for light and dark mode;
  • ranch (EOM): new implementation:
    • multi-sequence, multi-chain,
    • user-configurable angle database,
    • arbitrary distance constraints,
    • secondary structure components from NMR,
    • improved sequence alignment and reporting,
    • performance improvements;
  • sasrefcv/sasrefmx:
    • use updated library implementation of crysol,
    • performance improvements;
  • sasres: fixed FSC calculation;
  • shanum: changed internal GNOM routine to determine Dmax from GNOM4 to GNOM5;
  • sreflex: integrated updated crysol.
Discontinued Programs:
  • alpraxin (use cifop --shif-to-origin --align-axis instead);
  • damemb, damesv (use bodies in search volume mode instead);
  • damsel, damsup, damaver, damfilt, damclust (integrated into damaver);
  • dam2dam (use cifop --dam=R instead);
  • dam2en (use cifop --reflect-{x,y,z} instead);
  • dam2is, dam2alm (use crysol instead);
  • datshanum (use shanum instead);
  • supalm, supcomb, suppdb (use cifsup --method={ncc,nsd,rmsd} instead).

If you have any questions about the commercial ATSAS license please contact us at atsas@biosaxs.com.