Update help to match recent GUI changes (modes, extinct reflections & void maps)

Author: briantoby

MDhelp/docs/commontreeitems.md

@@ -129,7 +129,7 @@ Select the tab for the parameter type(s) you wish to constrain then create new p
 * **Add constraint** - If selected, a dialog box will appear with a list of the available parameters. Select one and press OK; a second dialog box will appear with only those parameters that can be used in a constraint with the first one. Choose those and press OK. Cancel in either dialog will cancel the operation. The equivalenced parameters will show as an equation of the form \(M1*P1+M2*P2+…=C\); the multipliers M1, M2, … and C can be changed via the 'Edit' button. The equation is shown in the window tagged by 'CONSTR' to mark it as a constraint equation assignment.
 * **Add New Var** - This behaves very much like the "Add constraint" menu command except that it defines a new parameter rather than define a value for the expression. That new var parameter can optionally have a named assigned. The expression is displayed with the keyword 'New Var' to mark its type. Note that a 'Refine?' box is included for this type of constraint.
 * **Make atoms equivalent** - This provides a shortcut for establishing constraints when two share a single site. Coordinates and Uiso values are constrained to be the same and site fractions are constrained to add to 1.
-* **Show ISODISTORT modes** - Used after a CIF from the ISODISTORT web site is read, which will display the values for the normal modes from representational analysis from the coordinates.
+   * **Show New Var modes** – When New Var constraints are present, this opens a window that shows the effect of the constraints to be seen. This is of particular value when representational analysis generated normal modes have been read from a CIF created with ISODISTORT.  From the created window,  the New Var parameters can be changed and the changes that the constraints make to the linked dependent parameters are shown. When this command is used from a Phase "Draw Atoms" tab rather than here, the structure plot is updated. The changes made here are temporary, unless the Save button is used to close the window. 
 
 In addition to menu commands, this window also offer the following actions by pressing buttons:
 

MDhelp/docs/phaseatoms.md

@@ -58,8 +58,7 @@ graphics window's structure drawing that is marked by crossing , red, green and
     * **Histogram bonds and angles** – plots histograms of bond lengths & angles about selected atoms.
     * **Apportion atom frac** – after selection of a 2nd element; this determines from atomic number and neutron scattering length the atom fractions of each type for selected atoms and presents results on the console.
     * **Density** – calculate density
-    * **ISODISTORT mode values** – when a structure has been imported from ISODISTORT,  this will compute the mode displacements for the current atom positions and display them in a popup window.
-
+   * **Show New Var modes** – When New Var constraints are present, this opens a window that shows the effect of the constraints to be seen. This is of particular value when ISODISTORT modes have been read.  From the created window,  the New Var parameters can be changed and the changes that the constraints make to the linked dependent parameters are shown. When this command is used from the "Draw Atoms" tab rather than here, the structure plot is updated. The changes made here are temporary, unless the Save button is used to close the window. 
 
 <a name="Phase-mouse-plotopts"></a>
 <H3 style="color:blue;font-size:1.1em">What can I do with the plot?</H3>

MDhelp/docs/phasedrawatoms.md

@@ -48,7 +48,6 @@ Many of the options below can also be accessed after selecting one or more atoms
    * **Fill CN-sphere** – using the atoms currently in the draw atom table, find all atoms that belong in the coordination sphere around the selected atoms via unit cell translations. NB: symmetry operations are not used in this search; do **Fill unit cell** first.
    * **Fill unit cell** - using the atoms currently selected from the draw atom table, find all atoms that fall inside or on the edge/surface/corners of the unit cell. This operation is frequently performed before Fill CN-sphere.
    * **Complete molecule** – beginning with a selected atom, transform other atoms to equivalent positions that form a contiguous molecule. Not appropriate for continuous structures (a warning will appear if the command is not completing)
-   * **Create void map** – by using a grid of probe positions, locate points outside of normal contact distances within a structure. Result is a mesh of small blue points in structural voids. These could indicate possible locations of missing solvent molecules or voids in porous materials. 
    * **Delete atoms** – Remove selected atoms from the draw atom table. If you remove all atoms, the table is then refilled from the Atoms table. You should do this operation after any changes to the contents of the Atoms table, e.g. if atoms are added or deleted.
    * **Update draw atoms** – refresh the drawn atom positions from the Atoms list,  You should do this operation after any changes to the contents of the Atoms table, e.g. by a structure refinement. This operates on all atoms and ignores any previous atom selection. 
    * **Load selected atoms** - refresh the selected  atom positions in the draw atoms list from the Atoms list.
@@ -60,6 +59,8 @@ The compute menu gives a choice of geometric calculations to be performed with t
    * **View pt. dist.** - this calculates distance from view-point to all selected draw atoms; result is given on the console window.
    * **Dist. Ang. Tors.** – when 2-4 atoms are selected, a distance, angle or torsion angle will be found for them. The angles are computed for the atoms in their selection order. The torsion angle is a right-hand angle about the A2-A3 vector for the sequence of atoms A1-A2-A3-A4. An estimated standard deviation is given for the calculated value if a current variance-covariance matrix is available. The result is shown on the console window; it may be cut & pasted to another application (e.g. Microsoft Word).
    * **Best plane** – when 4 or more atoms are selected, a best plane is determined for them. The result is shown on the console window; it may be cut & pasted to another application (e.g. Microsoft Word). Shown are the atom coordinates transformed to Cartesian best plane coordinates where the largest range is over the X-axis and the smallest is over the Z-axis with the origin at the unweighted center of the selection. Root mean square displacements along each axis for the best plane are also listed. The Z-axis RMS value indicates the flatness of the proposed plane. NB: if you select (e.g. all) atoms then Best plane will give Cartesian coordinates for these atoms with respect to a coordinate system where the X-axis is along the longest axis of the atom grouping and the Z-axis is along the shortest distance. The origin is at the unweighted center of the selected atoms.
+   * **Show New Var modes** – When New Var constraints are present, this opens a window that shows the effect of the constraints to be seen. From the created window,  the New Var parameters can be changed and the changes that the constraints make to the linked dependent parameters are shown. If these change atomic information, the structure plot is updated. The changes made here are temporary unless the Save button is used to close the window. This is of particular value when ISODISTORT modes have been read. 
+   * **Create void map** – by using a grid of probe positions, locate points outside of normal contact distances within a structure. Computed from the contents of "Atoms" list.  Result is a mesh of dots (actually small cubes) in regions of the structure with no atoms. These could indicate possible locations of missing solvent molecules or voids in porous materials. The GUI allows control over the size and density of the grid to be computed as well as how the map is displayed. The default provides small blue dots that may be hard to see on some monitors. 
 
 ### Menu '**Restraints**' Contents
 

MDhelp/docs/powdercells.md

@@ -31,7 +31,7 @@ To display a unit cell, possibly with space group extinctions, enter the unit ce
 
 To change the displayed extinctions, first set a Bravais class, which determines the unit cell type (see [list below](#Laue_List)), and then optionally select a space group (by default the highest symmetry space group for the class is selected). As any change is made to the unit cell values or the symmetry, the display of reflection positions shown in the plot window is immediately updated. The "Show hkl positions" button also forces an update of the plot, but this is normally not needed.
 
-Reflection positions are displayed as dashed vertical lines. Reflections will normally be shown as orange, but green lines are used instead in 3+1 superspace groups for reflections with non-zero components in the fourth dimension ("superlattice lines"). If the "Show extinct" option is selected, then reflections that are generated by the unit cell, but must be zero in intensity due to the selected space group are shown with blue dashed lines. This slows computations somewhat. Note that the speed of reflection display is determined by the number of reflections that are computed, so reducing the range of data used by changing the diffraction Limits will speed the refresh of the display when values/symmetry is changed.
+Reflection positions are displayed as dashed vertical lines. Reflections will normally be shown as orange, but green lines are used instead in 3+1 superspace groups for reflections with non-zero components in the fourth dimension ("superlattice lines"). If the "Show extinct" option is selected, then reflections that are generated by the unit cell, but must be zero in intensity due to the selected space group are shown with green dashed lines. This slows computations somewhat. Note that the speed of reflection display is determined by the number of reflections that are computed, so reducing the range of data used by changing the diffraction Limits will speed the refresh of the display when values/symmetry is changed.
 
 The reflection indices (hkl values) can be displayed by moving the mouse cursor over a reflection line and waiting ("hovering"). After a short delay, the indices for all nearby reflections are shown temporarily as a "tool tip". If multiple reflections are closely spaced, the reflection indices will be listed in the order that reflections occur, but extinct reflections are shown after non-extinct. Also, if multiple extinct reflections occur at the same location, only the first of them is used.