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EMBL Hamburg Biological
Small Angle Scattering
BioSAXS

DAMMIF manual

dammif

Written by D. Franke.
Post all your questions about DAMMIF to the ATSAS Forum.

© ATSAS Team, 2007-2016

Table of Contents

Manual

The following sections shortly describe the method implemented in DAMMIF, how to run DAMMIF from the command-line on any of the supported platforms, detail the dialog mode as well as the required input and the produced output files.

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

D. Franke and D. I. Svergun (2009). DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering J Appl Cryst. 42, 342-346.

Introduction

DAMMIF, a tool for rapid ab-initio shape determination in small angle scattering, is a reimplementation of the well known bead-modelling program DAMMIN.

In bead modeling a particle is represented as a collection of a large number of densely packed beads inside a search volume. Each bead belongs either to the particle or to the solvent. Starting from an arbitrary initial model DAMMIF utilizes simulated annealing to construct a compact interconnected model yielding a scattering pattern that fits the experimental data.

Please refer to the paper cited above for further details about the implemented algorithm.

Running dammif

Usage:

$ dammif [OPTIONS] [GNOMFILE]

OPTIONS known by DAMMIF are described in next section, the optional argument 'GNOMFILE' 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 GNOMFILE is given, the configuration is done in full interactive mode.

Command-Line Arguments and Options

DAMMIF accepts the following command line arguments:

ArgumentDescription
GNOMFILE The filename of a GNOM output, possibly with relative or absolute path components.

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

Short OptionLong OptionDescription
-p --prefix=<PREFIX> Prefix to prepend to output filenames. May include absolute or relative paths, all directory components must exist. Default is 'dammif'.
--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 DAMMIF 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.
-v --version Print version information and exit.
-h --help Print a summary of arguments and options and exit.

Interactive Configuration

If the optional argument 'GNOMFILE' is 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
GNOM input file? N/A Same as GNOMFILE-argument.
Angular unit? UNKNOWN Same as unit-option.
Output file prefix? dammif 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
Expected/assumed shape? Select one of: (u) unknown, (c) compact, (e) extended, (f) flat, (r) ring, (h) compact-hollow, (hs) hollow sphere, (rc) random chain (default: unknown) varvarvar The parameters of the starting model are based on the shape classification. An appropriate classification may significantely improve the reconstruction speed and accuracy as annealing parameters are adjusted by shape, e.g. extended particle generally require more summands in the spherical harmonics calculations.
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.
Proportion of the curve to be fitted? (0.0-1.0] 1.01.01.0 Proportion of the scattering curve to fit, starting at the first point.
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 DAMMIF 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-...) 0.010.010.01 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.

Runtime Output

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

Step:    1, T: 0.368E-03, 23/2287, Succ: 1062, Eval: 20002, CPU: 00:00:06
 Rf: 0.1504, Los: 0.39, Rg: 0.00, Cen: 0.00, Ani: 0.00, Fit: 0.1504

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

FieldDescription
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 fit of simulated data versus experimental data, 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.
Fit A function of Rf including all penalties and their respective weights. Decreases towards zero, the smaller the value, the better the fit.

dammif Input Files

Like DAMMIN, DAMMIF uses the distance distribution functions computed by GNOM as input files.

dammif Output Files

With each succesful run, DAMMIF 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.

ExtensionDescription
.log Contains the same information as the screen output and is updated during execution of the program.
-0.pdb
-1.pdb
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 Fit of the simulated scattering curve versus a smoothed-out version of the real-data. See dialog mode how to change the number of supporting points in the spline interpolation. Columns in the output file are: 's', 'Iexp' and 'Isim'.
.fir Fit of the simulated scattering curve versus the experimental data. Columns in the output file are: 's', 'Iexp', 'Errexp' and 'Isim'.
.in This file provides an easy way to re-run DAMMIF with the same set of input parameters (including random seed) to verify the effects of options or to re-run DAMMIF to get a chained PDB output.

Thus, if DAMMIF is started as

$ dammif --prefix=../foo/bar gnom.out

the files 'bar.log', 'bar-0.pdb', 'bar-1.pdb', 'bar.fit', 'bar.fir' and , 'bar.in' will be written in the directory '../foo', relative to the current working directory.

Examples

All examples use lyz.out as an input file, it is also included in the documentation directory of the installation package. Please note that the prefixes may be chosen arbitrarily. The values below are chosen for maximum clarity only.

A Quick Look

Use DAMMIF in FAST-mode to obtain a first model quickly:

$ dammif --prefix=lyz-fast --mode=fast lyz.out

More Detailed Reconstruction

Use DAMMIF in SLOW-mode get an improved reconstruction:

$ dammif --prefix=lyz-slow --mode=slow lyz.out

Customizing the Annealing Procedure

For best results, run DAMMIF in INTERACTIVE mode, customizing annealing parameters as required:

$ dammif --prefix=lyz-custom --mode=interactive lyz.out

Running dammif Multiple Times

On Linux, in bash syntax:

$ for i in `seq 1 10` ; do dammif --prefix=lyz-$i --mode=slow lyz.out; done

Make sure to use different prefixes when running DAMMIF multiple times in the same working directory. Further, if multiple DAMMIF-runs are started in parallel, e.g. on a cluster, make sure that the random seeds differ, otherwise identical results will be obtained.

Reproducing Results

Input-redirection can be used to let DAMMIF read settings from a configuration file

This example uses the .in-file of a previous run to obtain the exact same result, but this time, the dummy atoms shall be sorted to form pseudo-chains:

$ dammif --prefix=lyz-slow-chained --chained --mode=interactive < lyz-slow.in 

  Last modified: April 11, 2013

© BioSAXS group 2013