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• saspy: the Tk based plugin is outdated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 s_max 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 D_max 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.