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EMBL Hamburg Biological
Small Angle Scattering
BioSAXS
 

SASRES manual

sasres

Written by A.T. Tuukkanen
Post all your questions about SASRES to the ATSAS Forum.

© ATSAS Team, 2000-2016

Table of Contents

Manual

The following sections shortly describe the SASRES approach to asses resolution of ab initio model ensembles, how to run SASRES from the command-line on any of the supported platforms, describe the the required input files and parameters as well as the produced output file.

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

Anne T. Tuukkanen, Gerard J. Kleywegt and Dmitri I. Svergun(2016) Resolution of ab initio shapes determined from small-angle scattering IUCrJ. 3, 440-447.

Introduction

SASRES is a tool to assess the quality and resolution of ab initio shapes reconstructed using small-angle scattering (SAS) data. The novel Fourier Shell Correlation (FSC) based approach was developed to evaluate the resolution of an ab initio reconstruction using an ensemble of models. The variability of multiple SAS models derived from a single scattering dataset is utilized to estimate the model resolution. It was shown that the average FSC function over an ensemble that reflects the variability of models is directly related to the resolution of the individual models in the shapereconstruction.

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

Running Sasres

Usage:

$ sasres [OPTIONS] <FILES>

Here, the FILES argument is a list of PDBs. SASRES does not provide an interactive mode but is completely configurable through its command line options. The OPTIONS known by SASRES are described in the next section below.

Command-Line Arguments and Options

SASRES requires the following command line arguments:

ArgumentDescription
FILES The PDB files of ab initio models.

SASRES recognizes the following command-line options.

Short OptionLong OptionDescription
-m --modeltype=<b/r> Type of the ab initio models in an ensemble. Either a bead model (default) "b" or a dummy residue model "r".
-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 and should be disabled only in special cases.
-s --symmetry Specify the symmetry to enforce on the structures during superposition. All standard P-n-m symmetries are supported (Pn, n=1, ..., 19, Pn2, n=2, ..., 12) as well as P23, P432 and PICO (default: P1).
-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 for each structure pair (t01.pdb - t02.pdb),(t01.pdb - t03.pdb), (t02.pdb - t03.pdb) in the FSC computation. For example, when having three ab initio bead models t01, t02, and t03 in the ensemble:

$ sasres --modeltype=b t01.pdb t02.pdb t03.pdb
 Read file .............................................. : t01.pdb
 Number of atoms ........................................ : 2556
 Fineness of the structure .............................. : 2.200
 Read file .............................................. : t02.pdb
 Number of atoms ........................................ : 2534
 Fineness of the structure .............................. : 2.200

                                Initial       Final
              Orientation      Distance    Distance
             1     1     1       0.9100      0.7614
             1     1    -1       0.8862      0.7406
             1    -1     1       0.6914      0.6750
             1    -1    -1       0.6745      0.6652
            -1     1     1       0.8250      0.8166
            -1     1    -1       0.8395      0.8204
            -1    -1     1       0.7686      0.6722
            -1    -1    -1       0.7678      0.6981

                   Transformation matrix
        -0.6793      0.4418      0.5860     -0.2610
        -0.6304      0.0575     -0.7741     -0.0118
        -0.3757     -0.8953      0.2394     -0.4007
         0.0000      0.0000      0.0000      1.0000

 Wrote file ............................................. : t02_aw_t01.pdb

  ***   Evaluates scattering amplitudes from             ***
  ***   a dummy residues or a bead model.                ***
  ***   On the input the program prompts for the         ***
  ***   PDB file name containing the coordinates         ***
  ***   ( only CA atoms are to be read ),                ***
  ***   the type of the model ( DR or bead ),            ***
  ***   molecular weight of the protein in KDa,          ***
  ***   number of points in the reciprocal space,        ***
  ***   separation between them and the maximum          ***
  ***   order of harmonics to which the partial          ***
  ***   amplitudes will be calculated.                   ***
  ***   On the output calculated partial amplitudes      ***
  ***   are saved into the file specified by the User    ***
  ***   in CRYSOL format (ALM). This file can then be    ***
  ***   used i.e. for rigid body refinement in MASSHA).  ***
  ***   For the convinience the program also             ***
  ***   creates a DAT file with the same name which      ***
  ***   contains the corresponding scattering intensity. ***
  ***   Please note that the border layer is not         ***
  ***   taken into account.                              ***
  ***   Version 2.0 (r8897M)                             ***
  ***   Last revised  ---  12/19/14                      ***

 Number of atoms read ................................... : 2556
 Center of the molecule   :     0.0030  -0.0037  -0.0021
 Maximum radius ......................................... : 28.60
 Number of phases ....................................... : 1

 [...]

 t01.almt01.pdb
 t02_aw_t01.almt02_aw_t01.pdb
 Loading amplitudes...
 Intsum computation starts
 Comparing structures:
 t01.pdb  t02_aw_t01.pdb

 [...]
 

Here, the name of the read structure files and their number of atoms are reported together with the transformation matrix required for alignment and the details of computing FSC using spherical harmonics.

Sasres Input Files

SASRES requires at least an ensemble of three ab initio model PDB files as an input.

Sasres Output Files

Following a successful superposition of all models pairwise, SASRES computes the average FSC function and estimates the ensemble resolution. The results are given in a file called fsc.log providing the FSC function and corresponding resolution.


  Last modified: February 8, 2017

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