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:
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.
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.
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.
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).
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.
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.