Refine

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The sub-menu Refine is shown on the left. It allows:




LSQ

Least Squares Refinement.

LSQ info

Information about Least Squares calculations.

Restraints

Define and reset restraints.

DLSQ

Distance Least Squares Refinement.

Groups

Manage rigid body groups.

Thermal Factor

Select and delete atoms with a very high thermal factor.

Fourier

Fourier synthesis.

Hydrogens

Add or delete hydrogens.

Agreement

Produce statistics about agreement.

Compare Atoms

Compare coordinates of the current model with coordinates from an external file.


LSQ


Least Squares graphical interface is divided in 3 sections:


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 or Structure Factor Calculation only) and the Refinement 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 depending on user choices. The GO button will start the calculations.





In this section the user can fix or relax the atom parameters (coordinates, thermal factor) and set the thermal factor isotropic or anisotropic.





In the Rigid Body section the user can refine (or not) as Rigid Body the groups listed.



LSQ info


Information about Least Squares calculations such as atom coordinates, isotropic/anisotropic thermal factor, conditions on atom parameters (fixed, equivalence,..), last value of the residual are displayed.



Restraints


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.



DLSQ


Least Squares Calculation based on restrained distances



Groups



These menu items are related to the definition of groups of atoms to be refined as Rigid Body.

The Rigid Body interface allows, once a group of the list on the left has been selected, to associate the atoms of the group with the atoms of the current model.



Group Manager


At installation time a file, called Sir.gru, is created in the Home Directory of the user. It contains the groups of benzene and residues.

The user can add some customized group of atoms to be refined as Rigid Body.



Thermal Factor


During Least Squares calculations the value of the thermal factor for some atoms can assume too large values. This window can be used to analyse the values of the thermal factor and, eventually, delete the atoms whose value is too high.



Fourier


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 button.


Buttons

Help: this output.

Go: execute the Fourier synthesis.

Cancel: exit from Fourier interface.

Fourier type

Observed: The coefficients of the Fourier synthesis are the observed structure factors (Fobs).

2*Fobs Fcalc: The coefficients are two times the Fobs minus the calculated structure factors (Fcalc).

Fobs Fcalc: The coefficients are the difference between the observed minus the calculated structure factors.

Fourier Conditions

Peaks to add: The user can select the maximum number of peaks to be located.

Level (electrons/Å3): The peaks to be located must have the height greater than this value of the electron density.

Fourier Space

Unit Cell: The asymmetric part defined by the Space Group is the space where the Fourier synthesis has to be calculated.

Cube: The user can define a cube, having the faces parallel to the cell faces, where the Fourier synthesis has to be calculated. The dimension in Angstrom of the cube edge (default 2.0 Å) and the grid stepof the Fourier synthesis (default 0.20 Å) can be defined by the user. Using the mouse and moving the model, the user can put the cube where he wants.

If View Fourier map is checked, the Fourier map and the model are shown by the program Jav.

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:



Hydrogens


This menu item provides different approaches to add hydrogens to the model:



Hydrogens automatic generation.

Hydrogens aided generation.

Add hydrogens to a selected atom.

Delete all (generated) hydrogens.


If the automatic choice is selected, no user intervention is required. All the possible hydrogens will be generated on the basis of geometrical criteria.


Using the Wizard, the program checks distances and angles around atoms, 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.



Buttons

Help: this output

Accept: the current definitions are accepted and the next atom is selected

Stop: stops the modifications and generates hydrogens

Cancel: exit from the Wizard interface

On the right of the window it is supplied the list of candidate atoms for the H atoms generation. Only O, C and N atoms are considered.
The atom can be selected by clicking on a list item or using the buttons

On the left (Distances & Angles) , the geometry of the bonds corresponding to the current atom is visualized. The program determines and shows the hybriditation and the number of H atoms to be generated. It is possible to change the hybriditation, different from the suggested choice.
The number of H atoms to be generated can be changed only for N atoms.
It is possible to modify the default bond distances "current atom - H" (default: 0.960 Å).

By clicking on "Accept" the next atom will be considered.

The process ends when all atoms have been considered or when the "Stop" button is clicked.


Single: using this feature it is possible to generate hydrogen(s) bonded to a single atom. It is possible to use geometric considerations (in this case the program will suggest the possible hybridization) or it is possible to search hydrogens in a small volume of the map, around the selected atom.



If View Fourier map is checked, the Fourier map and the model are shown by the program Jav.

Hydrogens can also be generated using Jav.


Agreement


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.



Compare Atoms


If a structural model is available (i.e. solving a structure using electron diffraction data an X-Ray model could be available), it is possible to compare the coordinates provided by the program with the model.

Using the following window it is possible to load the model to compare:




The result of the comparison is shown below; the model is superimposed and drawn using dotted lines.


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