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Small Angle Scattering



Written by M.B. Kozin, updated by D. Franke
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Table of Contents


The following sections shortly describe the method implemented in ALPRAXIN, how to run ALPRAXIN from the command-line on any of the supported platforms, describe the interactive mode as well as the required input and the produced output file.

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

M.Kozin & D.Svergun (2001) Automated matching of high- and low-resolution structural models J Appl Cryst. 34, 33-41.


ALPRAXIN is a program to position a structure such that its principal inertia vectors are aligned with the coordinate axes. The structure can be a low-resolution bead model and/or a high resolution NMR or x-ray crystal structure.

The principal axes of inertia are calculated for a given set of atoms as eigenvectors of the inertia tensor. The structure is centered at the origin and rotated to have the principal axes aligned with the coordinate axes. The aligned structure is saved in the output file.

Please refer to the paper cited above for further details about the implemented algorithm.

Running alpraxin


$> alpraxin <FILE> [OPTIONS] 

ALPRAXIN accepts absolute as well as relative paths to the template PDB file.

In the interactive mode ALPRAXIN asks for the names of the input and output files and whether the enanthiomrph should be saved. The OPTIONS known by ALPRAXIN are described in the next section.

Command-Line Arguments and Options

ALPRAXIN requires the following command line arguments:

FILE The template PDB file.

ALPRAXIN recognizes the following command-line options.

Short optionLong optionDescription
-e --enantiomorphs Enable saving the enantiomorph e.g. a mirror image of the structure. By default this is disabled.
-q --quiet If enabled, informational console output is suppressed. Only errors, if any, will be printed.
-o --output=<FILE> Specify an output FILE where to write the moved and rotated model to. By default this corresponds to the basename of the second file plus r.pdb.
-v --version Print version information and exit.
-h --help Print a summary of arguments and options and exit.

Runtime Output

On runtime, the following lines of output will be generated to align the target structure 6lyz.pdb:

$ alpraxin 6lyz.pdb 
 Read file .............................................. : 6lyz.pdb
 Number of atoms ........................................ : 1102
 Fineness of the structure .............................. : 1.514

                   Transformation matrix
        -0.6406      0.3017     -0.7061      6.9967
        -0.0246     -0.9271     -0.3739     26.2582
        -0.7675     -0.2222      0.6013     -7.2986
         0.0000      0.0000      0.0000      1.0000

 Wrote file ............................................. : 6lyzr.pdb

The transformation matrix gives the rotation and translation of the input file to the coordinate axis.

alpraxin Input Files

ALPRAXIN requires one PDB files as input, the template structure The use of absolute and relative paths to the template PDB file is supported.

alpraxin Output Files

Following a successful superposition, ALPRAXIN creates a single output file for the aligned structure. By default the output filename is taken from the input target structure but is appended with 'r', eg.

$ alpraxin file1.pdb 

yields file1r.pdb as output. A different filename can be specified with the --output option.


Command-line execution

Use ALPRAXIN to align 6lyz.pdb, transform it into the mirror image and save in a named file:

$ alpraxin -e 6lyz.pdb -o 6lyz-e.pdb

The resulting structure will be written onto 6lyz-e.pdb.

  Last modified: July 18, 2017

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