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Structures Comparer window This utility calculates
root-mean-square distances (RMSDs) between two molecular structures. To use
this utility, one must firstly run 2 instances of Chemcraft application
(i.e. launch Chemcraft twice) and open a structure in each of them. The
structures can be opened in any way (e.g. through "File/Open" menu
item, or by typing atomic coordinates in Coord mode), but they must be
visible in Image mode of the corresponding windows. If the opened file
contains multiple geometries shown in the list at the left (e.g. for
optimization job), a specific element should be clicked at the list, to use
the geometry associated with exactly this element in the comparison. Then
"Tools/RMS compare structures" menu item should be choosen at any
of the two Chemcraft windows. The structures to be
compared must have equal numbers of atoms and atomic sequences. If the
structures have different atomic sequences, in one of them the atoms should
be reordered manually before using this utility ("Edit/Update sequence
by atomic labels" menu item can be used for this purpose). The minimized distances
between individual atoms in two structures are shown at the table. Below the
list of atoms, RMSD values for different types of atoms are shown (square
root of mean of squared distances for individual type of atoms). In the
"All atoms" row, the RMSD for all atoms in the molecule is shown.
In the "With weights" row, the RMSD calculated using specified
weights for individual atoms is shown (it is the square root of averaged
using the weights value of squared distances of all atoms). This value is
also shown below the table. Exactly this value is minimized in coordinates
transformation (see below). By default (when the "All atoms"
option is chosen, or all items are checked in the checklist at the left),
each atom has a weight of 1.0. In this case the values at "All
atoms" and "With weights" rows in the table are equal. If
"Specify types" or "Specify atoms" option is chosen,
unchecked atoms have 0.0 weights. The button "Use custom
weights" allows individual weights for atoms to be explicitly
specified. The weights do not need to be normalized. The button
"Recalculate" recalculates the RMSDs and shows them in the table. Algorithm: Before printing the RMSDs,
the program rotates and translates one of the structures to minimize the
RMSD value calculated with required weights of atoms. In current
implementation the rotation is made iteratively, with minimal step of 1E-18
rad. The error in RMSD caused by discrete rotation is approximately 1E-
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