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ATSAS release 2.8 is available

Posted: 2017.01.11 19:51
by AL
Download ATSAS 2.8
(academic users only)

New OS:
  • Ubuntu 16 and Debian 8 are now supported;
    Debian 6 is no longer supported;
    macOS installation became simpler.
New programs:
  • secplot - point-and-click interface to process SEC-SAXS data;
    sasres - resolution estimate of ab initio shape reconstruction;
    parcoor - partition protein coordinates (PDB) into subdomains according to dynamics (NMA);
    seqstat - get statistics about a protein from its amino acid sequence;
    pdbstat - get statistics about a protein in a PDB file;
    databsolute - normalise a SAXS curve to an absolute intensity scale;
    adderrors - simple tool to add simulated experimental errors to a dataset.
Removed programs:
  • supmon;
    autorgqw (use primus/qt instead);
    seq2mw (use seqstat instead);
    gnom version 4 is replaced by version 5 (formerly known as gnom5).
Changes in programs:
  • all:
    • improved random number generation (WELL512),
      filter out 'bad data' (e.g. with a negative standard error) from input data files,
      performance improvements with BLAS/LAPACK, kd-trees and reduced memory consumption,
      fixed typos and improved online help text, improved error handling and fixed reported issues,
      many improvements to libsaxsdocument;
    • increase the allowed maximum distance from the origin to 1000 Angstroms,
      loop-db now a single file in binary format (ATSAS now installs faster);
    • when using constant adjustment, add it to predicted curve, rather than subtracting from the experimental curve,
      more consistent reporting of the Rg values,
      skip rotamers when reading a structure,
      now supports all elements up to californium,
      allow up to 99th order spherical harmonics;
    cryson: allow up to 99th order spherical harmonics;

    dam2is: removed --fb option (order of Fibonacci grid);

    damaver: report model resolution as computed by SASRES;

    dammif: use shape classification with DATCLASS to choose starting shape;

    datgnom (version 5): default to a choice of the angular range so that Smax * Rg = 8;

    • avoid unnecessary rebin when merging datasets on identical s axes,
      improved merging if input files are on different s axis,
      improved scaling algorithm;
    datshanum: store Shannon fits within experimental angular range only;

    • allow overriding Rg and I(0) on command line,
      accept .dat/.int files;
    em2dam: simplified command-line interface, improved prediction of DAM and automatic threshold prediction;

    • add background to predicted curve, rather than subtracting from the experimental curve,
      include experimental errors in .fit files;
    monsa: improved format of output .pdb files;

    • added support for symmetry up to P9(2),
      increased maximum number of subunits to 15;
    • added support for superposing MONSA models,
      changed format of output transformation matrix to match supcomb;
    supcomb: added --proximity and --fraction options for fast calculations;

    ffmaker: allow arbitrarily many form factors;

    • HETATM entries are now incorporated,
      faster connectivity filter that considers all atoms,
      additional breaks score based on sequential connectivity,
      clashes score relative to molecular weight,
      added to report: RMSD to initial structure, new breaks and clashes scores,
      simplified user interface;
    • Rg, Chi2 and NSD values now reported to PyMOL console (mainly for Windows users),
      set working directory from configure tab (requested by Windows users),
      PDB coordinates are written to file for CRYSOL and SASREF runs.

Check ATSAS installation guidelines before updating ATSAS.
If you have questions or problems using ATSAS, please post your queries here.

ATSAS release 2.8.1 is available

Posted: 2017.05.24 14:48
by AL
Download ATSAS 2.8.1
(academic users only)

Changes in ATSAS 2.8.1:
  • reintroduced the legacy implementation of gnom as gnom4 due to unresolved issues with desmearing in gnom5;
    secplot - renamed to chromixs.
Changes in programs:
  • all: improvements to file handling and data parsing;

    • new option "--maxrg",
      improved Guinier interval search for data with unmasked beamstop;
    • update in element parsing of PDB,
      write error estimates to fit in interactive mode,
      improved performance with multiple inputs;
    cryson: ignore deuteriums if hydrogens are ignored;

    dam2alm: reduced memory usage;

    dam2is: updated default values;

    • actively try to minimize strands of single beads,
      improved initial dimensions of start models;
    datregrid: fixed alignment issues on "join";

    datadjust: do not merge template properties to output;

    • fixed a regression on model generation,
      ranch: fixed handling of percentage of symmetric structures;
    monsa: keep the project id;

    saspy: improvements for Windows PATH handling;

    • improved output on two MONSA input models,
      fixed issues with absolute file paths;
    • improved handling of non-ascii file names,
      fixed an issue when aborting an ab initio run,
      if present, show the smeared data while computing p(r),
      wizards remember the last used directory and files.

Check ATSAS installation guidelines before updating ATSAS.
If you have questions or problems using ATSAS, please post your queries here.

ATSAS release 2.8.2 is available

Posted: 2017.07.21 16:13
by AL
Download ATSAS 2.8.2
(academic users only)

Changes in programs:
  • chromixs: added Rg values estimation, export to vector graphics and option to close the project;
    databsolute: fixed error propagation;
    databsmw: apply values from Mylonas & Svergun 2007 as defaults;
    dammif: fixed issues with flat start model;
    dammin: significant performance improvements;
    damaver/damclust: significant performance improvements;
    gnom: fixed issues with slit smearing, overall improvements and fixes;
    primus/qt: allow 6 digits for slit smearing parameters;
    saspy: improvements in communications with alpraxin, crysol and supalm;
    sreflex: fixed some issues with nonstandard models and concoord refinement;
    shanum/datshanum: fixed estimates when zero errors are present;
    supcomb: significant performance improvements;
    sasdoc/manuals: general updates.

ATSAS release 2.8.3 is available

Posted: 2017.12.06 11:23
by AL
Download ATSAS 2.8.3
(academic users only)

This is the last release for the following platforms:
  • Ubuntu 12;
    openSUSE 13.
Changes in ATSAS 2.8.3:
  • New program datmw:
    • unified access to multiple estimates of molecular weight;
    • added entry to Start and applications folders for each platform,
      added molecular weight estimation/plotting;
    • use actual residue and chain numbers in contacts conditions reporting,
      use different chain ids for symmetry mates;
    • fixed issues with determination of number of supporting knots,
      increase bead size of models based on "hollow" classification;
    • improved shape classification,
      predict Dmax and MW from experimental data;
    • crysol wizard: fixed default arguments,
      Molecular Weight wizard: new;
    • support for PyMOL 2.0;
    • new option to work with neutron data (SANS),
      improved performance with large structures.
Check ATSAS installation guidelines before updating ATSAS.
If you have questions or problems using ATSAS, please post your queries here.

ATSAS release 2.8.4 is available

Posted: 2018.05.28 11:16
by AL
Download ATSAS 2.8.4
(academic users only)

New platforms (beta): Debian 9 and Ubuntu 18.04.
This is the last release for Debian 7.
Due to incompatibilities of Qt4 with recent versions of MacOSX, there are no GUI programs (primus, chromixs etc.) in the MacOSX package of ATSAS 2.8.4.

Changes in ATSAS 2.8.4:

New programs:
  • dammix: restoring the shape of unknown component in an evolving system;
    pddffit: fits a given pair distance distribution function to experimental data;
    datft: direct Fourier transform of experimental data to pseudo pair-distribution function.
Changes in programs:
  • dammif:
    • added sanity checks to some input parameters,
      minor performance improvements;
    • improved error reporting,
      fixed output of structural neighbours on --query;
    datcmp: allow alpha=0 to skip the clique-finding step;

    datmw: fixed output of MW if any of the base method fails;

    • fixed output format of last column,
      support up to 20 components;
    • removed limitation to 500 points in Guinier region,
      fixed input range of fields to determine MW from relative scale;
    primus/quickwin: general updates;

    • improved error reporting,
      fixed incorrect example in help output;
    sasdoc/manuals: manual updates;

    saspy: improved remote control of sasref on Windows.

    sasflow: added support for datclass and datmw, general improvements;

    radaver: improved median filter of outliers.