DOT Utility Programs Reference Manual

Section 1: Preprocessing Utilities

The following utilities are described in the section "Using DOT", and descriptions are not duplicated here.

• transh
• striph
• gen_uhbd_com
• run_uhbd
• pdb_to_vol
• pdb_to_dot

Purpose

Creates the 3x3 rotation matrix from Eulerian angles and prints the matrix in the single-line format ( 9 matrix elements in one row, separated with "space" symbol ).

Usage

    dotmatrix theta phi psi > stdout

Parameters

• theta, phi, psi - Eulerian angles (in radians) of the rotation; theta is in the range [0,Pi], phi and psi are in the range [-Pi,Pi].

Purpose

Translates the PDB file to the grid origin (coordinates 0, 0, 0).

Usage

    pdbcenter < original_pdb_file > translated_pdb_file

Parameters

• original_pdb_file - a PDB-format file with the molecule to be translated;
• translated_pdb_file - the PDB-format file with the centered molecule.

Purpose

Calculates the displacement of the molecule geometrical center from the grid origin (coordinates (0, 0, 0)); prints the displacements along X, Y, Z axes, separated with "space" symbol.

Usage

    pdbmcom < pdb_file

Parameters

• pdb_file - a PDB-format file.

Purpose

Rotates the molecule by applying a 3x3 rotation matrix.

Usage

    pdbrot rotation_matrix < original_pdb_file > rotated_pdb_file

Parameters

• rotation_matrix - 9 elements of the rotation matrix, separated with "space" symbol.
• original_pdb_file - a PDB-format file with the molecule to be rotated;
• rotated_pdb_file - the PDB-format file with the rotated molecule.

Purpose

Translates the molecule to the specified location.

Usage

    pdbtrans X Y Z < original_pdb_file > translated_pdb_file

Parameters

• X, Y, Z - the displacements along x, y, z axes;
• original_pdb_file - a PDB-format file with the molecule to be translated;
• translated_pdb_file - the PDB-format file with the translated molecule.

Purpose

Translates the molecule to the specified location and then rotates it applying the rotation matrix.

Usage

    pdbrottrans rotation_matrix X Y Z < original_pdb_file > output_pdb_file

Parameters

• rotation_matrix - 9 elements of the rotation matrix, separated with "space" symbol;
• X, Y, Z - the displacements along x, y, z axes;
• original_pdb_file - a PDB-format file with the molecule to be transformed;
• output_pdb_file - the PDB-format file with the transformed molecule.

Purpose

Converts a free PDB format file into the strict PDB format file.

Usage

    pdbform < original_pdb_file > output_pdb_file

Parameters

• original_pdb_file - a free PDB format file to be transformed;
• output_pdb_file - the strict PDB format file.

Section 2: Postprocessing Utilities

Purpose

Generates a set of PDB-format files according to the specified positions and orientations of the moving molecule; the positions (x, y, z coordinates) and orientations (Eulerian angles) are taken from fields #2-5 and #6-8 of the DOT output file; the names for the output PDB-format files are created by appending the current line number (in the DOT output file) to the base name specified as an argument.

Usage

    pdbgen original_pdb_file output_base_name dot_dat_file

Parameters

• original_pdb_file - a PDB-format file with the moving molecule;
• output_base_name - the base file name for the PDB-format files;
• dot_dat_file - a selection from the DOT output file in "dat" format (energy X Y Z theta phi psi).

Purpose

Traslates and rotates the moving molecule to the position and orientation specified by a DOT output record (in "dat" format: energy X Y Z theta phi psi).

Usage

    pdbfromdot X Y Z theta phi psi < original_pdb_file > output_pdb_file

Parameters

• original_pdb_file - a free PDB format file to be transformed;
• output_pdb_file - the PDB-format file with the transformed molecule.

Purpose

Cuts off and prints the positions of the moving molecule which are inside the specified ball, cube, or cylinder from the DOT output file in "dat" format (energy X Y Z theta phi psi) or in "e3d" format (partition_sum X Y Z).

Usage

    butcher

Parameters

• the utility works in an interactive mode: the user is asked to supply needed parameters.

Purpose

Extracts the electrostatic energy and solvent excluded volume values, along with the corresponding positions and orientations, from DOT log files; prints the two corresponding files with name extension ".xbump" (excluded volume) and ".xelectro" (electrostatic energy); each line in the output files contains the following data: the current orientation (theta phi psi); the best electrostatic energy; the best solvent excluded volume; the best weighted sum of the above; the corresponding x, y, z coordinates.

Usage

    extr base_name

Parameters

• base_name - the generic file name (without .log extension) for the current DOT run.

Purpose

Builds the histogram for the distribution of a specified field from DOT output files; the output file contains the following data:

• minimal value
• maximal value
• the size of the intervals (increment value)
• the left boundaries of the intervals (the 1st column)
• the frequencies in the intervals (the 2nd column)
• the corresponding bars (represented as a sequence of "*" symbols)

Usage

    histogr input_file field bins > output_file

Parameters

• input_file - any DOT output file
• field - the field number to be analysed
• bins - the number of intervals for the histogram