Superimposer
Introduction
The Superimposer plugin is used to move some target set of atoms by a
computed amount. In practise two sets of atoms are usually used to
compute the transformation that is added to the coordinates of target set atoms.
Superimposer provides currently three different computation methods.
The possible computations are:
- Center - compute the position of geometrical center of all atoms in Set1.
Use the inversion of the position vector as the transformation. Each atom in the target set
is moved by that amount.
- Vertaa - use VERTAA algorithm to compute the transformation that would
superimpose Set2 of (Ca-atom) residues on Set1. The Set2 may contain more than
one proteins. Each Chain of Set2 will be used in turn to compute the transformation, then
all selected atoms from that protein will be moved. Thus, multi-chain proteins will superimpose
by their last chain. If a chain in Set2 is from the same protein as Set1, only the chain will move.
- Iterate - iteratively refine structural alignment. The structures must be superimposed on
start. Superimposition will be adjusted and a structural alignment object is created, if the
iteration converges. The alignment will only have pairs within the Cut-off distance - not
the full sequences. Both the gap penalty and the Cut-off distance can be set by the user.
- Superimpose - use existing pairwise alignment (as Set1) to define pairs of residues,
and compute the transformation that would minimise the RMSD over all those (Ca-atom) pairs.
As in Vertaa, each chain (but the first one) will be pairwise superimposed over the first chain.
- RMSD - use existing pairwise alignment (as Set1) to define pairs of residues,
but this time include every pair of atoms from those residues where atoms have the same name and
the atom in first chain is selected. Compute the transformation that would minimise the RMSD over
all those atom pairs.
As in Vertaa, each chain (but the first one) will be pairwise superimposed over the first chain.
- Norm For each selected molecule take selected atoms, compute covariance matrix of atomic
coordinates, solve eigenvectors (PCA), and use them to rotate the molecule. The direction, where
atoms are most separate should line up with x-axis. (EXPERIMENTAL)
The selection of Sets is similar in all cases, but the contents of each Set
depends on the current mode of computation. The buttons will on Press event search
all selected objects of correct type from the Bodil data and store them in internal list.
In Align mode the Set1 button provides a list of Alignments in Bodil to select from.
The Apply button will compute the transformation and apply it to the target set.
The OK button what Apply button does, and closes the window.
The Cancel button simply closes the window.
Configuration file entries
There are no configurable options at this moment.
Contents