point group window
"Edit/Set point group" menu items allows the atomic
coordinates in molecule to be adjusted to a specified point group. This
feature can be very helpful for creating input files, because symmetrical
molecules are computed much faster then unsymmetrical.
Before using this utility, the molecular geometry must be set
sufficiently close to the required point group. Special attention must be
paid to long chains in molecule, because small changes of angles or
dihedrals in them can lead to significant displacements of atomic
coordinates from symmetrical positions. The conformations of symmetry unique
fragments must correspond to each other. "Drag fragments" mode is
very convenient for adjusting chains.
At the "Set point group" window Chemcraft shows a list of
groups with different axes orientations, appropriate to apply. The
"R" value is a root-mean-square displacement of atomic
coordinates, necessary to apply a specific group. Usually the group with
lowest R value (at the top of the list) is most appropriate to choose.
If a complex point group cannot be identified, one can firstly choose
apply subgroups (Cs, Cn) and then set the whole group.
In some cases, groups shown in the list include groups with
incorrectly identified symmetry unique atoms. After applying such group, the
molecule becomes distorted. Usually such false groups have much higher R
value than "normal" groups. If
such symmetry is set, Ctrl+Z should be pressed.
For very big molecules, sometimes the groups are not identified at once by Chemcraft. In this case it can be useful to specify the "Random rotations" algorithm of group identification: "Edit/Set point group/Group identification algorithm/Random rotations mode". This mode will eventually identify any group, but maybe not at the first try (choose "Edit/Set point group/group name" multiple times with this mode).