Plot part 4

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3. View ASER

Vista 2.0 incorporates a much more compact ASER viewer than was present in version 1.0. The 4 menus of version 1.0 have been combined into just 1 menu, as shown above. There are now 3 display windows allowing 1D, 2D and 3D representations to be viewed simultaneously. The large window on the left is the active window, and by default displays the 3D representation of the molecule. The 1D or 2D information can be exchanged with the 3D image by clicking in either the 1D or 2D windows. When the 3D display is not in the active window certain geometrical functions become disabled, but it is still possible to rotate, translate, etc.

The lower part of the ASER viewer menu contains the operations available to the user. These are described in detail below.

3.1 Refcodes

Selected refcodes exported from the Spreadsheet or Plot menus are shown in the scrolling refcode list in the bottom-left of the window. The order of the refcodes is unchanged from that exported from the Spreadsheet and Plot lists.

Only one refcode can be viewed at a time and this is the one highlighted in the list. Initially this will be the first refcode. The entry can be changed by clicking on another entry in the list (direct access) or by pressing the -/+ keys to move sequentially through the list.

The selected entry is displayed in all 3 windows.

3.2 Parameter Values

The values for all the parameters for the selected fragment/refcode are shown in this scrollable list. If the ASER viewer was called from the Plot menu then the parameters involved in the plot will be highlighted in the list.

3.3 Atom Pick Mode (APM)

A bank of radio buttons Label Atom, Calc. Dist., Calc. Angle, Calc. Tors. and No Action determine the action taken when atoms are selected for the 3D representation of the molecule only (the 3D representation must be in the active window).

By default the APM is Label Atom. The three geometric modes will direct the user to select a number of atoms and the appropriate calculated value is returned in the dialogue bar directly below the active window.

No Action performs no action.

3.4 Render Options

The render options available in the ASER viewer menu are applicable only when the 3D representation of the molecule is in the active window. These options are exactly the same as those of the same name found in the Quest program. All of the options are operated by a toggle button.

Unit Cell
displays the 3D crystal diagram as it is located in the outlined unit cell.

displays the unit cell contents as a packing diagram. The Unit Cell check box mimics the packing button. This is because the packing routine, by default, adds the cell. The user can, however, switch off the cell manually.

toggles the display of hydrogen atoms in the 3D crystal diagram.

labels all atoms in the 3D crystal diagram.

toggles the display of the element key box in the active window.

Bond Colour
The colour coding mode for the 3D stick diagram. The Quest options of Element, Bond Type, Fragment and Residue are included. The Fragment button is greyed out if no FGN file or FGD files are located.

3.5 3D Molecule Manipulation

The 3D representation of the molecule can be manipulated using the buttons in the bottom-right section of the ASER viewer menu. Manipulation does not require the 3D representation to be in the main window.

Molecule Rotation
there are 6 rotation buttons for the independent rotation about each of the three axes. The rotation increment is displayed above, in a text field. The value can be changed by the -/+ keys, which will increment the current value by 1.0. Alternatively, the user can type directly into the field. Values between 0.0 and 180.0 are permitted.

Molecule Translation
the translation buttons are analogous to the rotation buttons. The translation increment is 0.1, with limits of 0.0 and 2.0.

3.6 Miscellaneous

refreshes the display

launches the Help pop-up menu. See section 7 for further details.

resets the 3D view to the least squares projection.

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Correlation and Covariance Spreadsheet .