SUPCOMB, is a program to superimpose one 3D structure onto another.
These structures can be low-resolution bead models and/or high resolution NMR or x-ray crystal structures.
The alignment of shape models (ie. *.flm files) is not supported.
Please note: there used to be two versions of SUPCOMB, named supcomb13 and supcomb20, implementing slightly different matching algorithms.
The two separate programs got merged into a single SUPCOMB program.
The program represents each input structure as an ensemble of points, then minimizes a normalized spatial discrepancy (NSD) to find the best alignment of two models.
NSD is a measure of quantitative similarity between sets of three-dimensional points and is calculated in the following way:
Briefly, if two three-dimensional models are represented as a set of points, for every point in the first set (model 1), the minimum value among the distances between this point and all points in the second set (model 2) is
found, and the same is done for the points in the second set. These distances are added and normalized against the average distances between the neighboring points for the two sets.
For ideally superimposed similar objects, NSD tends to 0; it exceeds 1 if the objects systematically differ from one another.
Please refer to the paper cited above for further details about the implemented algorithm.
This option specifies the metric for the proximity measure between two models.
It can be the standard normalized spatial discrepancy ('NSD') metric or the overlapped volume ('VOL') metric.
The latter metric can be applied for large macromolecular complexes (with MW about 1MDa or larger) in order to speed up the calculations
(for details see the SUPALM article).
By default the proximity metric is set to 'NSD'.
This option specifies the part of the structure closer to the surface to take for calculations with the 'NSD' metric.
It can be set between 0 and 1 (in the latter case the whole structure will be taken into account).
The lower fraction can be applied for large macromolecular complexes (with MW about 1MDa or larger) in order to speed up the calculations
(for details see the SUPALM article), but it is recommended to set it higher than 0.3.
By default the fraction is set to 1.0.
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).
Please note: symmetry constraints are only applied in slow mode.
SUPCOMB requires two PDB files as input. A template structure and a target structure for alignment/superposition. The use of absolute and relative paths to the template and target PDB files is supported.
Following a successful superposition, SUPCOMB creates a single output file for the superimposed target structure. By default the output filename is taken from the input target structure but is appended with 'r', eg.
$ supcomb file1.pdb file2.pdb
yields file2r.pdb as output. A different filename can be specified with the --outputoption.
To superimpose 10 structures onto a single template, on linux, in bash syntax:
$ for i in `seq 1 10` ; do supcomb template.pdb file-$i.pdb; done
If one has unnumbered files to superimpose, on linux, in bash syntax:
$ for file in "a.pdb b.pdb c.pdb d.pdb" ; do supcomb template.pdb $file; done
where template.pdb is the reference/template structure.
Note that when one has a large collection of structures for superposition, the program DAMAVER is optimised for a fast superposition of multiple structures, automatically choosing the most representative structure.