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.



  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- 14 A for molecules of 50-100 atoms (the larger a molecule, the higher this error is).