ATSAS release 3.0 is available

ATSAS for Windows, Linux and Mac, general installation issues, ATSAS online etc.
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ATSAS release 3.0 is available

#1 Post by AL » 2019.11.01 14:40

Download ATSAS 3.0
(academic users only)

Supported platforms:
  • Windows 7, 8 and 10;
  • macOS 10.12 Sierra, 10.13 High Sierra, 10.14 Mojave;
  • Ubuntu 16 and 18;
  • Debian 9;
  • Red Hat/CentOS 7.
New programs:
  • cif2pdb - converts mmcif files to pdb format; temporary module to use for ATSAS programs that are not yet mmcif-compatible;
  • damemb - generates cubic search volume for membrane proteins;
  • elllip - generates ellipsoidal model of a liposome;
  • bilmix - modelling of polydisperse unilamellar lipid vesicles with asymmetric density profiles;
  • lipmix - modelling of polydisperse unilamellar/multilamellar lipid vesicles;
  • datmif - ab initio modelling directly to experimental SAS data, without p(r);
  • datresample - statistically correct resampling of experimental data frames;
  • nmator - normal mode analysis in torsion-angle space; optimized for nucleic acid structures;
  • imsim - simulates 2D scattering data from calculated scattering intensity from crysol (.abs);
  • im2dat - radial averaging of 2D images to 1D scattering patterns;
  • imop - image operations similar to datop, e.g. addition, subtraction etc;
  • flexbin - quaternary structure modelling of a dimeric complex formed by flexible subunits.
Removed programs:
  • checkcomplex;
  • adderrors.
Changes in programs:
  • all: general fixes and improvements;
  • bunch: keeps a list of up to 100 best solutions;
  • pre_bunch:
    - added mmcif support,
    - improved sequence alignment and output on error;
  • crysol:
    - added internal border layer computation,
    - added anomalous scattering computation,
    - output of calculated scattering on an absolute scale (.abs);
  • crysol 3.0:
    - added capability for user-defined contrast multipliers,
    - added support for dummy beads,
    - output of calculated scattering on an absolute scale (.abs);
  • dattools: validated and improved error propagation;
  • damesv/monsa: liposome generation enabled;
  • gasbori/gasborp/gasbormx: outputs the monomer and oligomer intensities;
  • pdbtools (pdb2seq, pdbstat, seqstat):
    - improved PDB parsing,
    - added mmCIF support;
  • primus/qt:
    - improved (de-)smearing support and added all system types of gnom,
    - improved residual analysis for model-model and model-data fits,
    - improved plot configuration and export,
    - performance improvements;
  • saspy:
    - added support for crysol calculations with explicit hydrogens,
    - modified to be python 2 and 3 compatible.

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Re: ATSAS release 3.0 PrimusQT Plots

#2 Post by mawhite » 2019.11.05 20:07


The new Primus(QT) plots (on Linux) are terrific. There is much greater flexibility in in plotting styles and the plots are almost ready for publication. The one remaining issue is the inability to adjust the Font Size of the axis numbering. The numbering font could be tied to the axis Label font to produce great plots.

There is one other feature I would request. Is it possible for PrimusQT to read a configuration file (.XML) with the default Plot Styles? I would define default colour and Symbol/Line styles. For instance when reading a FIT file the first Data Entry would be Symbol only, and the Fit Entry a Line only. With such an ability making publication quality plots would be quick and simple.

Best regards,

Posts: 3
Joined: 2019.11.07 23:26

Re: ATSAS release 3.0 is available

#3 Post by ThiagoVSeraphim » 2019.11.07 23:45


The interface and functionality of the new ATSAS 3.0 is indeed terrific.
I noticed that a new program, FLEXBIN, has been released within the ATSAS package. I am wondering if there is further references about FLEXBIN, besides its manual.
I would be glad for any extra information shared.


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Joined: 2007.08.03 19:16

Re: ATSAS release 3.0 is available

#4 Post by SaxsMax » 2019.11.11 10:54

Hi Thiago, so far there is no publication dedicated to FlexBin

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ATSAS release 3.0.1 is available

#5 Post by AL » 2020.02.12 20:44

Download ATSAS 3.0.1
(academic users only)

New platform: Debian 10.

Framework changes: updated to Qt-5.12.6 and QtIFW-3.2.0:
  • fixes the issue of numpad not working in primus/qt on Linux;
  • fixes black text on black widget installer on MacOS with dark mode;
  • fixes issues with the ATSAS environment variable on Windows.
Changes in programs:
  • coral: print errors to stderr instead of stdout;
  • damaver: fixes issues calling external dam2alm binary;
  • databsolute: fixed error propagation;
  • datft: extrapolate input data to high angles;
  • datmw: fixed wording of incorrect error message, fixed range check that may lead to ignoring Vc or MoW results;
  • imsim: added support for user-defined background scattering;
  • lipmix: fixed calculations of the structure factor of multilamellar vesicles;
  • nmator: fixed pool generation in instances where the same file was generated multiple times, fixed directory creation on Windows;
  • oligomer: do not lose precision of input data;
  • pdb2seq: fixed handling of malformed input files;
  • saspy: removed ATSAS version check;
  • sreflex: fixed build-error that made sreflex unusable (macOS-only);
  • supalm: added verification that the CRYSOL binary is in the PATH;
  • supcomb: improved performance on model-regrid in fast mode;
  • primus/qt:
    • main plot: fit remaining data to window on data set remove,
    • Guinier analysis: reduced size of normalized Kratky plot,
    • Guinier analysis: made display of standard error of Rg more consistent,
    • comparison: fixed inverted sign of residuals,
    • Distance Distribution: fixed axis labels for leaf and rod case,
    • documents list: improved handling of scaling factors and increased range.

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ATSAS release 3.0.2 is available

#6 Post by AL » 2020.06.18 11:37

Download ATSAS 3.0.2
(academic users only)

Changes in programs:
  • crysol:
    • do not attempt to automatically re-calculate scattering in dialogue mode if the number of harmonics is considered insufficient,
    • fixed atomic form factors of Rhenium and Osmium;
  • crysol 3: ask for contrast multipliers in dialogue mode only;
  • dammif: added a command-line option for shape class: use '--shape=unknown' to override incorrect classifications;
  • dammin: added command-line options for custom search volumes and their parameters;
  • damsel: added check that at least two input files are provided;
  • ffmaker: do not require errors in files with (likely) experimental data;
  • gajoe: verify that size list has as many entries as junXXX.eom;
  • nmator:
    • fixed redirection of CRYSOL output,
    • decreased motion amplitudes in pool generation mode to reduce nonviable models;
  • oligomer: fixed a mistake introduced in 3.0.1 where oligomer would ignore multiple input files;
  • pdb2seq:
    • fixed out of bounds error on missing element column,
    • output 'X' if an unknown residue is encountered;
  • primus/qt:
    • fixed opening of data files clicked in Finder (macOS only),
    • automatic update of the plot on modification of data scale factors;
  • sreflex:
    • fixed issues with non-default locale,
    • do not do refinement if nucleotides are present;
  • all GUIs (macOS only): improved visuals on high-DPI displays;
  • Legacy/massha: install missing support files

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ATSAS release 3.0.3 is available

#7 Post by AL » 2020.10.28 11:31

Download ATSAS 3.0.3
(academic users only)

New platforms: CentOS 8 and Ubuntu 20.
This is the last Ubuntu 16 release.
This is the last Windows 32-bit release. Future Windows releases will be 64-bit only.

Changes in programs:
  • bodies: added option to predict scattering on "absolute scale", i.e. assuming the body has the average density of protein;
  • crysol: fixed an issue where nucleotides were not recognised when parsing the PDB file;
  • databsolute: allow user to set or override the temperature value and report used temperature scaling coefficient in the footer of the output file;
  • datft: added command-line options 'decay' and 'stop-at-zero', fixed file property output;
  • datmerge: merge duplicate s-values for each input file before merging all input files;
  • gajoe: fixed a memory corruption that may have resulted in incorrectly reported Rsigma values;
  • saspy: updated reported version number;
  • sreflex: fixed an issue with locale settings where the decimal separator is not a '.'.

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ATSAS release 3.0.4 is available

#8 Post by AL » 2021.09.05 15:38

Download ATSAS 3.0.4
(academic users only)

New PyMOL plugin:
  • mpbuilder: membrane-protein support application.
Changes in programs:
  • bodies:
    • fixed calculation of volume of rotation ellipsoid,
    • fixed calculation of hard-sphere structure-factor,
    • fixed crash on calculation of hard-sphere structure-factor for s==0.0;
  • bunch: increased length of output file names;
  • crysol: report wrong input file format, return non-zero exit code on invalid input data;
  • dammif:
    • six significant digits in .fit output file,
    • removed overcompensation for bead size when shape is estimated to be extended;
  • dammin:
    • increased default number of annealing steps in fast and slow mode,
    • added chain identifier and fixed column alignment in PDB output file,
    • output files in current working directory,
    • increased maximum number of data points read from GNOM file;
  • em2dam:
    • verify that the selected threshold is in map range,
    • reduced overall memory usage,
    • additional error checks;
  • ffmaker: fixed missing default values in dialog mode;
  • gasbor:
    • added chain identifier and fixed column alignment in PDB output file,
    • output files in current working directory,
    • fixed endless loop with invalid input file,
    • fixed endless loop that occurred when started on the command line with nDR > 8000;
  • gajoe (EOM):
    • use individual amino acid form-factors instead of average,
    • fixed calculations in 'gajoe --pool' mode;
  • nmator: fixed memory initialization in special cases;
  • oligomer: verify that a form-factor file has been specified and that it is not also used as a data file;
  • ranch (EOM):
    • do not "forget" ranch log file name,
    • fixed crash on missing arguments,
    • properly error out on empty sequence,
    • do not calculate intensities for sequences with less than 70AA due to numerical inaccuracies; use gajoe instead;
  • sasres (damaver): fixed FSC calculation, removed adjustment to determine resolution;
  • sasrefcv: handle malformed contacts-condition file more gracefully;
  • sreflex: do not fail at the RESTRAINED refinement stage on Windows 64 bit.

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