Generated to Input
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Dialog Box - called from: Transform menu

This converts the generated atoms (i.e., all those generated by the symmetry operations and translations within the given boundaries) to input atoms, removes all symmetry and boundary conditions, and changes to a special operating mode, called "Input=generated". This is like converting the current generated volume to a molecule with no symmetry.

This option is required before using the Multiple Structures options in the Transform menu. It is also a good idea to use this option if you want to delete more than a few generated atoms (see Deleting Atoms).

Temperature factor data are carried over into the special mode as Cartesian eigenvalues and vectors rather than U or beta coefficients, but they can no longer be modified. However, if there is more than one structure fragment temperature factors are not allowed (they will be deleted).

Orientation radio buttons. You have the option of returning to the original or standard orientation before converting, or taking the current orientation as the new "original" orientation. This orientation will be saved, which was not the case in pre-V4.0 ATOMS.

Some of the following checkboxes may not be shown, depending on circumstances.

Convert molecules to fragments. This will convert molecules or groups located in several different ways to individual fragments. If one of the Molecules in Crystal boundary options has been chosen, all atoms will be in molecules, and each molecule will become a fragment. "Molecules" may be individual atoms, as in CaCO3 structures (assuming Ca-O bonds are not defined or are marked as intermolecular). If another boundary option is used, and molecules or groups are subsequently located with the Find button in the Generated Atom Data dialog (which appears when you click on an atom), or with the Locate Groups dialog in the Transform menu, there may be atoms which are not part of molecules or groups. All these "leftover" atoms will be put into a single fragment, in addition to those already located.

Remove non-plotting atoms. Non-plotting atoms are those which have been explicitly marked as non-plotting, either individually or in groups. Also classed as non-plotting atoms in PDB (protein) structures are hetatoms and/or waters which have been omitted from the plot by means of the setting in the PDB (Protein) Display Parameters dialog in the Input2 menu. Atoms in incomplete polyhedra, which may or may not be shown in the drawing (Polyhedra dialog, Input1 menu) are in a separate option below.

Keep thermal ellipsoids. Thermal ellipsoids are not allowed in Multiple Structures, so there is no point in keeping them if additional fragments are to be added.

Omit atoms in incomplete polyhedra. This includes all atoms in polyhedra which have less than the specified number of ligands, i.e. are incomplete because of boundary conditions.

Keep vectors. Atomic vectors are not likely to be useful in Multiple Structures.

In early versions of atoms in Input=generated mode there were no separate lists of input and generated atoms, because of memory constraints. Rotations of the complete structure acted directly on the input atoms (not a separate list of generated atoms), and thus when the structure was saved the rotations were permanent. Currently, rotations act on a separate list of generated atoms, and do not affect the input atoms. However, if you rotate or translate individual fragments with options in the Multiple Structures Dialog or the DialogBar-Fragments, these will permanently affect the input atoms.