Alignment
QMView may be used to align two structures and calculate differences between
the volumetric data of the structures. Given two similar structures and,
for example their corresponding electron densities:
I
II
The two sturctures may be superimposed on one another to examine the difference
in a particular property. The user selects three atoms from each molecule
and is given a choice of 3 options:
1. Force the planes defined by the three chosen atoms of each molecule into the
same plane,force the second atom of one molecule onto the second
atom of the second molecule and fit the remaining 2 degrees of freedom.
2. Force the planes defined by the three chosen atoms of each molecule into the
same plane,place the second atom of one molecule onto the second
atom and allow the user to interactively move one structure in the plane
of the second.
3. Force the planes defined by the three chosen atoms of each molecule into the
same plane,force the second atom of one molecule onto the second
atom of the second molecule and force the vertex defined by atoms 1 and 2
of molecule 1 onto the vertex defined by atoms 1 and 2 of molecule 2.
In the figure below, the two structures are superimposed using option 1:
In the figure, the green surfaces represent the positive differences
between I and II while the red surfaces represent
the negative differences. Interpertation of the above figure is
straighfoward: Structure I has an imidazole ring while structure II
does not. Hence the surface around the imidazole ring. It can be
seen that the other surfaces are mainly due to parts of the molecule
not lining up exactly.