• Manual
  • Introduction
  • Running dammix
    • Command-Line Arguments and Options
    • Interactive Configuration
    • Runtime Output
  • dammix Input Files
  • dammix Output Files
• Examples
  • Intermediate states for time-resolved data series
  • Monomer-multimer equilibrium
  • Multiple assembly states

Manual

Introduction

DAMMIX reconstructs the shape of an unknown component in an evolving system and estimates the volume fractions of all components at each measured condition. The initial and final states of the system are assumed to be known or approximated from theoretical or experimental scattering data.

The program uses an ab initio bead modeling approach similar to DAMMIF and searches for the most compact bead model whose linear combinations with the known initial and final states best fit the SAXS data. Volume fractions are determined using the same algorithm as in OLIGOMER.

Running DAMMIX

Usage:

$ dammix [OPTIONS] [SASDATA(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:

The first and second positional arguments define the initial and final system states. Both these states can be provided either as experimental SAS data (.dat) or as atomic model in .pdb or .cif format. If an atomic model is provided, the corresponding theoretical scattering curve is calculated and used as the known component of the system.

All remaining positional arguments (3rd, 4th, …) are considered experimental curves for intermediate conditions; DAMMIX reconstructs the unknown component and estimates volume fractions for each curve. For two-component mixtures, set the second argument to none (this exact string).

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

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.

An interactive answers file (.ans) may be used to record and replay configurations, enabling repeatable runs without re-entering parameters.

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

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:

DAMMIX Input Files

CRYSOL reads one or more experimental SAS data (.dat) files.

The first two arguments may alternatively also be atomic models in either .pdb .cif or .ent format.

See Command-line Arguments and Options for a note on the implied meaning of positional arguments.

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.

Examples

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 --unit=2

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=1

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