Plot part 4
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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,
The lower part of the ASER viewer menu contains the operations available to
the user. These are described in detail below.
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.
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.
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
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.
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.
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.
- 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.
- 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.
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- refreshes the display
- launches the Help pop-up menu. See
section 7 for further details.
- resets the 3D view to the least squares projection.
Correlation and Covariance Spreadsheet