The sub-menu Refine is shown on the left. It allows:
| LSQ | Least Squares Refinement |
| LSQ info | Information about Least Squares calculations |
| Thermal Factor | Select and delete atoms with a very high thermal factor |
| Restraints | Define and reset restraints |
| Cell Content | Modify the unit cell content |
| Tables | Produce some table useful for publications |
| Fourier | Fourier synthesis |
| Hydrogens | Add or delete hydrogens |
| Agreement | Produce statistics about agreement |
Least Squares graphical interface is divided in 4 sections: General, Modify Atoms Parameters, Equivalence and Define Blocks. The program provides default values but the user can change them. In the first section the user defines the Least Squares strategy (Diagonal Matrix, Full Matrix, Block or Structure Factor Calculation only) and the conditions such as Damping Factor, Reflections cutoff, number of cycles. 18 Weighting Schemes are available and their parameters can be modified. At the bottom of this window information about the ratio Observations/Parameters is updated dependig on user choices. The GO button will start the calculations.
The user can fix or relax the atom parameters (coordinates, thermal factor) and set the thermal factor isotropic or anisotropic. In order to apply changes the user has to select the action and the selection method as shown in the animation below:
On the right of the window the list of selected atoms is is provided.
It is possible to equivalence parameters of different atoms through the use of a coefficient. The following window provides an easy way to do it. In the List of Equivalece conditions are displayed all the conditions already defined. It is possible to delete them by selecting with the mouse and by clicking on Delete button.
When the number of parameters to refine is too high, the user can divide them in blocks. By means of the following window it is possible to associate atom parameters to different blocks, increase or decrease the number of blocks and specify which block will contain the scale factor.
Information about Least Squares calculations such as atom coordinates, isotropic/anisotropic thermal factor, conditions on atom parameters (fixed, equivalenced,..), last value of the residual are displayed.
During Least Squares calculations the value of thermal factor for some atoms can assume too large values. This window can be used to delete such atoms.
An efficient way to improve the ratio Observations/Parameters during Least Squares calculations is the use of Restraints. They are managed through the following interface. Once some restraint has been defined, it is shown on the graphic window. As an example a restrained angle has been defined below.
During the refinement the unit cell content declared can change (solvent molecules etc.) By means of this window the user can add/delete atomic species and modify the number of atoms in the unit cell.
It is possible to prepare tables suitable for publications. Also CIF file can be produced.
In order to locate new atoms, a Fourier interface is available. Once the Fourier type has been selected and the number of new peaks has been decided, the calculations are started by clicking on GO button.
The peak search routine provides a number of new peaks. Information about peak intensity and distance from the closest atom is provided by means of the window below, so the user can select peaks to retain:
New peaks are represented by stars:
and a toolbar is available to manage the new peaks:
The user can use the following tools:
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Information about the selected peak or atom |
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Modify the Plot Style of the model |
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Change species to selected peak or atom |
Peaks not re-labelled will be discarded.
The following features allow the user to generate or delete hydrogens:
| Automatic | Hydrogens automatic generation |
| Wizard | Hydrogens aided generation |
| Single | Add hydrogens to a selected atom |
| H Bridge | Hydrogen bridge |
| Delete | Delete all hydrogens |
Automatic:
no user intervention is required. All hydrogens bonded to carbons will be generated on the basis of geometrical criteria.
Wizard:
the program checks distances and angles around a carbon atom, supplies this information and suggests the possible hybridization; the user can accept the hint or modify the hybridization, can skip the current atom or abort the Wizard procedure.
All carbon atoms will be automatically checked by the program. At the end of the Wizard procedure the user will be prompted to generate or not hydrogens:
Single:
hydrogens will be (immediately) generated bonded to the atom selected by the user
H Bridge:
hydrogens can be generated as Hydrogen Bridge.
Delete:
the user has to confirm the action:
Statistic on agreement are important to improve the refinement. It is possible to show or omit reflections with respect to a selected condition or class.
