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:
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.
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.
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.
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).
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'.
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).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
The fields can be interpreted as follows, top-left to bottom-right:
Field
Description
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.
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 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'.
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.
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.
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'.
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.
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.
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):
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:
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:
