Manual

The following sections briefly describe 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.

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”) models, and (c) provide an averaged, filtered model suitable as a search volume input for DAMMIN, also known as DAMSTART model.

Given several ab initio models in .pdb or .cif 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 the need to call external programs. The most representative model is determined, and outliers 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 are removed (damfilt model), and surrounded by a solvent shell to make it suitable as a start model for DAMMIN (damstart model).

Note that none of the models generated, damaver, damfilt or damstart will not 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 coordinate files of ab initio models in .pdb or .cif format. DAMAVER accepts absolute as well as relative paths.

Command-Line Arguments and Options

DAMAVER requires the following command line arguments:

Argument	Description
FILE(S)	Two or more atomic or dummy atom models in .pdb or .cif format.

DAMAVER recognizes the following command-line options.

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>	Maximum order of harmonics; default: 20, minimum: 1, maximum: 100. This defines the resolution of the calculated curve. The default value should be sufficient in most use cases. For large or extended particles higher orders could improve the results, at the cost of an increased run time. This value must be increased whenever the maximum scattering angle is increased (smax).
	--ns <N>	Number of calculated data points; default: 101, maximum = 10001.
	--smax <SM>	Maximum scattering angle in inverse angstroms, either for calculating the theoretical curve up to SM or for fitting to SM; default: 0.5\(\AA^{-1}\), maximum: 2.0\(\AA^{-1}\)
-p	--prefix=<FILE>	The PREFIX to prepend to any output filename; default: damaver
	--model-format	Output format of 3D models, one of: cif, pdb; default: cif
-h	--help	Print a summary of arguments, options, and exit.
-v	--version	Print version information 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 coordinate files or dummy atom models as input. Each may be either in .pdb or .cif format.

damaver Output Files

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

Suffix	Description
-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. Lists models included or rejected in the global averaging done. Names the most representative model overall that also fits the experimental data.
-global-damaver.pdb -global-damaver.cif	The average of all ‘Included’ models in pdb or mmCIF format, depending on the model-format option. The calculated scattering of this model does in general not fit the experimental data.
-global-damfilt.pdb -global-damfilt.cif	The averaged model with low occupancy beads removed models in pdb or mmCIF format, depending on the model-format option. The calculated scattering of this model does in general not fit the experimental data.
-global-damstart.pdb -global-damstart.cif	The filtered model with solvent beads added in pdb or mmCIF format depending on the model-format option. This model is suitable to be used as a start model for DAMMIN. The calculated scattering of this model does in general not fit the experimental data as-is. However, the final model generated by DAMMIN may.
-clusterXXX-summary.txt	The summary of XXXth cluster. Lists models included or rejected in the averaging done for this cluster. Names the most representative cluster model that also fits the experimental data.
-clusterXXX-damaver.pdb -clusterXXX-damaver.cif	The average of all ‘Included’ models of clusterXXX in pdb or mmCIF format, depending on the model-format option. The calculated scattering of this model does in general not fit the experimental data.
-clusterXXX-damfilt.pdb -clusterXXX-damfilt.cif	The averaged model of clusterXXX with low occupancy beads removed models in pdb or mmCIF format, depending on the model-format option. The calculated scattering of this model does in general not fit the experimental data.
-clusterXXX-damstart.pdb -clusterXXX-damstart.cif	The filtered model of clusterXXX with solvent beads added in pdb or mmCIF format depending on the model-format option. This model is suitable to be used as a start model for DAMMIN. The calculated scattering of this model does in general not fit the experimental data as-is. However, the final model generated by DAMMIN may.

Example

Average a set of models using the Normalized Spatial Discrepancy (NSD) as a metric. All output models are created in PDB format.

damaver --method nsd --model-format pdb t01.pdb t02.pdb t03.pdb t04.pdb t05.pdb t06.pdb t07.pdb t08.pdb t09.pdb t10.pdb t11.pdb