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.

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

Argument Description
FILE(S) Two or more atomic or dummy atom models in PDB or mmCIF format.
Short Option Long Option Description  
  --method=<NAME> One ofNSD, NCC, or ICP; default: ICP. SeeCIFSUPfor 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 whenmethod=NCC. Maximum order of harmonics; default: 5, minimum: 1, maximum: 100. SeeCRYSOLfor details.  
  –ns=<N> Only used whenmethod=NCC. Number of calculated data points; default: 101, maximum = 10001. SeeCRYSOLfor details.  
  –smax=<SM> Only used whenmethod=NCC. Maximum scattering angle inÅ^-1^; default: 0.5Å^-1^, maximum: 2.0Å^-1^. SeeCRYSOLfor details.  
-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 atomic coordinate files or dummy atom models as input. Each may be either in PDB or mmCIF 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 themethodselected.
-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{.cif, .pdb} The average of all ‘Included’ models in pdb or mmCIF format. The calculated scattering of this model does in general not fit the experimental data.
-global-damfilt{.cif, .pdb} The averaged model with low occupancy beads removed models in pdb or mmCIF format. The calculated scattering of this model does in general not fit the experimental data.
-global-damstart{.cif, .pdb} The filtered model with solvent beads added in pdb or mmCIF format. This model is suitable to be used asstart model forDAMMIN. The calculated scattering of this model does in general not fit the experimental data however, the final model generated by DAMMIN does.
-clusterXXX-summary.txt The summary of the XXXth cluster. Lists models included or rejected in the averaging done for this cluster. Names the most representative model of this cluster that also fits the experimental data.
-clusterXXX-damaver{.cif, .pdb} The average of all ‘Included’ models of clusterXXX in pdb or mmCIF format. The calculated scattering of this model does in general not fit the experimental data.
-clusterXXX-damfilt{.cif, .pdb} The averaged model of clusterXXX with low occupancy beads removed in pdb or mmCIF format. The calculated scattering of this model does in general not fit the experimental data.
-clusterXXX-damstart{.cif, .pdb} The filtered model of clusterXXX with solvent beads added in pdb or mmCIF format. This model is suitable to be used as start model forDAMMIN. The calculated scattering of this model does in general not fit the experimental data however, the final model generated by DAMIN does.

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"