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Small Angle Scattering

DAMAVER manual


Written by D. Svergun and M. Petoukhov, updated by D. Franke.
Post all your questions about DAMAVER to the ATSAS Forum.

© ATSAS Team, 2001-2022

Table of Contents


The following sections briefly describes DAMAVER, how to run DAMAVER from the command line, as well as the required input and the produced output files. Previously, DAMAVER used to have a set of companion applications, DAMSEL, DAMSUP, DAMFILT, DAMSTART and DAMCLUST. The functionality of all these have been merged into DAMAVER for ease of use.

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

V. V. Volkov and D. I. Svergun (2003). Uniqueness of ab-initio shape determination in small-angle scattering. J. Appl. Cryst. 36, 860-864.


DAMAVER is an application to (a) align ab initio low resolution models e.g. provided by DAMMIF, DAMMIN or GASBOR; (b) select the most typical ("probable") model; and (c) and provide averaged, filtered and model suitable as search volume input for DAMMIN (a.k.a. DAMSTART model).

Given several ab initio models in PDB or mmCIF format, the program first superimposes all possible pairs by applying one of the methods for superposition of models that are available in CIFSUP, namely NSD, NCC or ICP, without need of calling externals programs. The most representative model is determined, and outlier are excluded from subsequent calculations. The aligned models are remapped onto a grid of densely packed beads in order to compute a frequency map. For each bead, the cross volume with proximal dummy atoms in the input models (occupancy) is computed and saved into the output file (damaver model). This model is also filtered, i.e. unlikely beads removed (damfilt model), and surrounded with a solvent shell to make it suitable as a start model for DAMMIN (damstart model).

It is to note that none of the models generated, damaver, damfilt or damstart will generally fit the experimental data. Use the damstart model with DAMMIN to obtain a final model that fits the data.

Running damaver


$ damaver [OPTIONS] <FILE(S)>

Here FILE(S) may be two or more atomic coordinate files of ab initio models in PDB or mmCIF format. DAMAVER recognizes the following command-line arguments and options.

Command-Line Arguments and Options

FILE(S) At least two atomic coordinates files in either PDB or mmCIF format.

Short Option Long Option Description
--method=<NAME> One of NSD, NCC, or ICP; default: ICP. See CIFSUP for details.
-e --enantiomorphs=<YES|NO> Enable/disable the search of enantiomorphs, i.e. either one of a pair of molecules that are mirror images of each other but are not identical. By default this is enabled.
--nbeads=<N> Overall number of beads within the resulting DAM; default: 5000
--lm=<N> Only used when method=NCC. Maximum order of harmonics; default: 5, minimum: 1, maximum: 100. See CRYSOL for details.
--ns=<N> Only used when method=NCC. Number of calculated data points; default: 101, maximum = 10001. See CRYSOL for details.
--smax=<SM> Only used when method=NCC. Maximum scattering angle in Å-1; default: 0.5Å-1, maximum: 2.0Å-1. See CRYSOL for details.
-p --prefix=<FILE> The PREFIX to prepend to any output filename; default: damaver
-o --version Print version information and exit.
-h --help Print this help text and exit.

Mandatory arguments to long options are mandatory for short options, too.

Runtime Output

DAMAVER does not have any runtime output.

damaver Input Files

DAMAVER requires two or more atomic coordinate files of ab initio models as input. Each may be either in PDB or mmCIF format.

damaver Output Files

All output files start with prefix and appended suffix; -clusterXXX files are optional and only created if more than one cluster was determined (a single cluster would be identical to -global).

-distances.txt A table of all pairwise distances. Distance values depend on the method selected.
-global-summary.txt The summary of all inputs, assuming no clusters.
-global-damaver.cif The average of all 'Included' models.
-global-damfilt.cif The averaged model with low occupancy beads removed.
-global-damstart.cif The filtered model with solvent beads added, suitable to be used as start model for DAMMIN.
-clusterXXX-summary.txt The summary of the XXXth cluster.
-clusterXXX-damaver.cif The average of all 'Included' models of clusterXXX.
-clusterXXX-damfilt.cif The averaged model of clusterXXX with low occupancy beads removed.
-clusterXXX-damstart.cif The filtered model of clusterXXX with solvent beads added, suitable to be used as start model for DAMMIN.

  Last modified: April 11, 2013

© BioSAXS group 2013