EMBL Hamburg Biological
Small Angle Scattering

DAMMIX manual


Written by P.V. Konarev and D.I. Svergun.
Post all your questions about DAMMIX to the ATSAS Forum.

© ATSAS Team, 2005-2018

Table of Contents

  • Examples
  • Manual


    DAMMIX program represents the algorithm for restoring the shape of unknown component in the evolving system together with the volume fractions of the components at each recorded condition. The initial and final states of the systems are assumed to be known or can be reasonably well approximated by theoretical or experimental scattering pattern. The method uses ab initio bead modelling procedure similar to DAMMIF and yields the most compact bead model for which the linear combinations with the initial and final states of the systems provide the best overall fit to SAXS data. The volume fractions are found using the same algorithm as in OLIGOMER.

    If you use results from DAMMIX in your publication, please cite:

    P.V. Konarev and D. I. Svergun. (2018) Direct shape determination of intermediates in evolving macromolecular solutions from small-angle scattering data. IUCr Journal, 5, 402-409.

    Running DAMMIX


    $ dammix [OPTIONS] [DATAFILE(S)]

    OPTIONS known by DAMMIX are described in next section, the optional argument 'DATAFILE(S)' in the section on input files.

    In general, command-line options can be used to make choices about the properties of the particle to reconstruct, while the interactive configuration is used to govern the annealing process.

    If neither OPTIONS nor DATAFILE(S) is given, the configuration is done in full interactive mode.

    Command-Line Arguments and Options

    DAMMIX accepts the following command line arguments:

    DATAFILE(S) The filename of a DATA file(s), possibly with relative or absolute path components. The first and the second argument can be in the format of scattering curve (DAT file) or PDB model (PDB file), for the latter case the theoretical scattering curve calculated from this model will be used as known component of the system. It is RECOMMENDED to input the experimental data with the angular axis units in invesre ANGSTROMs.

    DAMMIX recognizes the following command-line options. Mandatory arguments to long options are mandatory for short options too.

    Short OptionLong OptionDescription
    --omit-solvent Pass this option to disable the output of solvent PDB files
    -m --mode=<MODE> Configuration of the annealing procedure, one of FAST (bigger beads, cooling down quickly), SLOW (smaller beads, cooling down slowly), or INTERACTIVE. Default is 'INTERACTIVE'. See example.
    -s --symmetry=<NAME> Specify the symmetry to enforce on the particle. Any P-n-m symmetry known by DAMMIN is supported (Pn, n=1, ..., 19 and Pn2, n=2, ..., 12). Cubic and icosahedral symmetries are not available. By default, no symmetry is enforced (P1).
    -a --anisometry=<NAME> If, due to prior studies, it is known that the particle's shape shall be either PROLATE or OBLATE, one may use the anisometry option to enforce a penalty on particles that do not correspond with the expected anisometry. By default, anisometry is 'UNKNOWN'.
    -u --unit=<UNIT> Angular units of the input file, one of ANGSTROM or NANOMETER. By default, an attempt is made to estimate the unit scale.
    -q --quiet Suppress screen output, write a .log-file only. By default, all runtime information is printed to screen and the .log-file.
    -c --chained By default, dummy atom models are written to .pdb-files in random order. The maintainers of the Proteine Data Bank expect the atoms to be ordered in (pseudo-)chains prior to submission. With this flag DAMMIX attempts to order the output according to this requirement. See also the example on how to reproduce results. Please note: the implemented chaining algorithm is quite basic and may take a long time for large models.
    --constant=<VALUE> Specify a user defined constant to subtract; 0 to disable constant subtraction. If unspecified, a constant to subtract is automatically determined.
    --volume Activation of the manual input for excluded Porod volumes for each individual input curve.
    --max-bead-count=<NUMBER> Maximum number of beads in search volume (unlimited if undefined).
    -v --version Print version information and exit.
    -h --help Print a summary of arguments and options and exit.

    Interactive Configuration

    If the optional arguments 'DATAFILE(S)' are omitted, settings available through command-line arguments and options may also be configured interactively as shown in the table below. Otherwise these questions are skipped.

    Screen TextDefaultDescription
    Number of experimental curves? 5 Total number of experimental curves including the initial and final states of the system. Defualt value is set to 5.
    DATA input files? N/A Same as DATAFILE-argument. The first argument corresponds to the initial state of the system (e.g. monomer), the second argument to the final state (e.g. aggregate), one can use for them both experimental data files (DAT) or PDB models (PDB) formats. The rest of the agruments should represent experimental scattering curves.
    Angular unit? UNKNOWN Same as unit-option.
    Output file prefix? dammix Same as prefix-option.
    Create pseudo chains in PDB output? NO Same as chained-option.
    Expected particle symmetry? P1 Same as symmetry-option.
    Expected particle anisometry? UNKNOWN Same as anisometry-option.
    Simulated annealing setup? SLOW Same as mode-option.

    In 'INTERACTIVE'-mode a list of parameters governing the annealing process may be fine-tuned:

    Screen TextDefaultFAST-mode Setting SLOW-mode SettingDescription
    Dummy atom radius? [1.0-?] [Angstrom] varvarvar The estimate for the dummy atom radius is based on Dmax to result in a search volume of about 2.000 (FAST-mode) to about 10.000 (SLOW-mode) beads. The smaller this radius is set, the more beads are generated, the slower the process.
    Maximum number of spherical harmonics? [1-50] 201520 The more harmonics, the more accurate the reconstruction becomes, but the slower the process. Very elongated particles may require up to 50 harmonics, quick screening can be done as low as 10-15. The default values may be adjusted by shape classification.
    Number of knots in the curve to fit? [1-?] varvarvar Experimental data is smoothed by spline interpolation before fitting. This defines the number of supporting points of the spline. By default, twice the number of Shannon Channels is used, but a minimum of 20.
    Curve weighting function? Select one of: [l]og, [p]orod, [e]mphasised porod, [n]one emph. porodemph. porodemph. porod Weighting function to ensure a better fit at lower angles. If unsure, use the default.
    Initial random seed? varvarvar To reproduce results, re-use the random seed. Default value is time-based. If multiple runs of DAMMIX shall be started at the same time, use an input file with different random seeds.
    Maximum number of temperature steps in annealing procedure? [1-?] 200200400 Stop if simulated annealing is not finished after this many steps. The more iterations per step and the slower the system is cooled, the more temperature steps are required.
    Maximum number of iterations within a single temperature step? [1-?] 200.00020.000100.000 Finalize temperature step and cool after this many iterations at the latest.
    Maximum number of successes per temperature step before temperature is decreased? [1-?] 20.0002.00010.000 Finalize temperature step and cool after at most this many successful phase changes.
    Minimum number of successes per temperature step before temperature is decreased? [1-?] 2002050 Stop if not at least this many successful state changes within a single temperature step can be done.
    Temperature schedule factor? [0.0-1.0) 0.950.90.95 Factor by which the temperature is decreased; 0.95 is a good average value. Faster cooling for smaller systems is possible (0.9), but slower cooling (0.99) needs to be applied more often. The default factor is increased for extended particles.
    Rg penalty weight? [0.0-...) 0.0010.0010.001 How much the Rg Penalty shall influence the acceptance or rejection of phase changes. A value of 0.0 disables the penalty. If unsure, use the default value.
    Center penalty weight? [0.0-...) 0.000010.000010.00001 How much the Center Penalty shall influence the acceptance or rejection of phase changes. A value of 0.0 disables the penalty. If unsure, use the default value.
    Looseness penalty weight? [0.0-...) How much the Looseness Penalty shall influence the acceptance or rejection of phase changes. A value of 0.0 disables the penalty. If unsure, use the default value. If unlike smooth surfaces and sharp edges are observed, try decreasing this penalty weight.
    Anisometry penalty weight? [0.0-...) 0.0/0.50.0/0.50.0/0.5 How much the Anisometry Penalty shall influence the acceptance or rejection of phase changes. A value of 0.0 disables the penalty. If unsure, use the default value, 0.0 if no anisometry was specified, 0.5 otherwise.
    Minimum volume fraction penalty weight? [0.0-...) 0.0/0.50.0/0.50.0/0.5 To keep the minimum volume fraction of unknown component not below 3% (over all curves). A value of 0.0 disables the penalty. If unsure, use the default value. If the volume fractions of uknown component are too high, try decreasing this penalty weight.
    Oligomer volume penalty weight? [0.0-...) 0.0/0.50.0/0.50.0/0.5 Applied for two-components systems when the oligomeric state of the restoring component is known. A value of 0.0 disables the penalty. If unsure, use the default value.

    Runtime Output

    On runtime, two lines of output will be generated for each temperature step:

    Step:    4, T: 0.238E-04, 723/2500, Succ: 2000, Eval: 13840, CPU: 00:00:15
     Rf: 0.1954, Los: 0.10, Rg: 0.27730E+01, Cen: 3.04, Ani: 0.00, Mfr: 0.00,
     Vol: 0.45011E+01 Fit: 0.2048

    The fields can be interpreted as follows, top-left to bottom-right:

    Step Step number. Starts at 1, increases monotonically.
    T Temperature measure, starts at an arbitrary high value, decreases each step by the temperature schedule factor.
    N/M N beads in phase particle in M beads overall.
    Succ Number of successful phase changes in this temperature step. Limited by the minimum and maximum number of successes. The number of successes should slowly decrease, the first couple of steps should be terminated by the maximum number of successes criterion. If instead the maximum number of iterations per step are done, or the number of successes drops suddenly by a large amount, the system should probably be cooled more slowly.
    Eval Accumulated number of function evaluations.
    CPU Elapsed wall-clock time since the annealing procedure was started.
    Rf Goodness of overall fit of simulated data versus experimental data (to all experimental data curves), does not take penalties into account.
    Los Contribution of Looseness Penalty, not taking the Looseness Penalty Weight into account.
    Rg Contribution of Rg Penalty, not taking the Rg Penalty Weight into account.
    Cen Contribution of Center Penalty, not taking the Center Penalty Weight into account.
    Ani Contribution of Anisometry Penalty, not taking the Anisometry Penalty Weight into account.
    Mfr Contribution of Minimum Fraction Penalty for the uknown component, not taking the Minimum Fraction Penalty Weight into account.
    Vol Contribution of Volume Penalty for the uknown component (to be used for two-component mixtures when the oligomeric state of the restoring component is known), not taking the Volume Penalty Weight into account.
    Fit A function of Rf including all penalties and their respective weights. Decreases towards zero, the smaller the value, the better the fit.

    DAMMIX Input Files

    DAMMIX uses the experimental data files as input files. The first and the second argument define the initial and the final state of the system, respectively. They can represent experimental data or PDB models from which the theoretical scattering will be calculated and used as known component. The other arguments (3rd, 4th etc) will correspond to the experimental data seria for which the shape of the uknown component and the volume fractions of all components will be restored. In the case of two-component mixtures (e.g. monomer-multimer equilibrium) the second argument has to be set to 'none'.

    DAMMIX Output Files

    With each succesful run, DAMMIX creates a set of output files, each filename starts with a customizable prefix that gets an extension appended. If a prefix has been used before, existing files will be overwritten without further note.

    .log Contains the same information as the screen output and is updated during execution of the program.
    The model is written in two parts: '-0.pdb' contains the beads of the solvent (a.k.a. the search volume), '-1.pdb' represents the modelled particle. The REMARK sections of both files contain information about the application used and about invariants of the particle, e.g. Rg, volume and molecular mass of the particle. If omit-solvent was specfied the output of the -0.pdb file is omitted. If chained output was requested, the dummy beads in '-1.pdb' are laid out in pseudo-chains.
    .fit Fits from the three (or two)-component mixtures (using the restored shape of the unknown component and restored volume fractions of all components) versus each individual experimental data curve (except the first two curves in the command line argument list that correspond to the known system states). Columns in the output file are: 's', 'Iexp' and 'Ifit'.
    .dat Two files: components_best.dat and fractions_best.dat that contain the restored scattering patterns from the components of the mixture and the restored volume fractions of the components for each experimental curve.

    Thus, if DAMMIX is started as

    $ dammix data1.dat data2.dat data3.dat data4.dat --prefix=mixt1 

    the files 'mixt1.log', 'mixt1-0.pdb', 'mixt1-1.pdb', 'data3_best.fit', 'data4_best.fit' as well as 'components_best.dat' and 'fractions_best.dat' will be written in the currten working directory.


    Please note that the prefixes in the examples may be chosen arbitrarily. The values below are chosen for maximum clarity only.

    Intermediate states for time-resolved data series

    Use DAMMIX in FAST-mode to obtain a first model quickly for 14 hours insulin fibrillation time seria (the initial and final states of the system corresponds to r1.dat and r14.dat):

    $ dammix r1.dat r14.dat r2.dat r3.dat r4.dat r5.dat r6.dat r7.dat r8.dat
    r9.dat r10.dat r11.dat r12.dat r13.dat --prefix=insulin --mode=fast

    Monomer-multimer equilibrium

    Use DAMMIX in SLOW-mode to get an improved reconstruction for two-component concentration dependent NGF seria (mixture of dimers and dimers of dimers), the initial state is calculated from ngf.pdb (dimer model), the final state is described by 'none' in order to account for two-component mixture:

    $ dammix ngf.pdb none ngf1.dat ngf2.dat ngf3.dat ngf4.dat ngf5.dat
    --prefix=ngf --mode=slow --unit=angstrom

    Multiple assembly states

    For best results, run DAMMIX in INTERACTIVE mode, customizing annealing parameters as required. This is an example of multiple assembly states of lumazine synthase that forms icosahedral capsids of T1 (Dmax=18 nm) and T3 types (Dmax=30 nm), the restored shape corresponds to the dissociated free facets of the capsids:

    $ dammix t1.pdb t3.pdb lym1.dat lym2.dat lym3.dat lym4.dat lym5.dat
    lym6.dat lym7.dat lym8.dat lym9.dat lym10.dat
    --prefix=lym --mode=interactive 

      Last modified: May 28, 2018

    © BioSAXS group 2018