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

• Manual
  • Introduction
  • Running damaver
    • Command-Line Arguments and Options
    • Runtime Output
  • damaver Input Files
  • damaver Output Files

Manual

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.

Introduction

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

Usage:

$ 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

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).