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;