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1 | | -## Draw Options |
2 | | - |
3 | | -<H3 style="color:blue;font-size:1.1em">What can I do here?</H3> |
4 | | - |
5 | | -The Draw Options window provides access to a number of items that control how the structure is displayed. If a map is available (Fourier of charge flipping), one can display a 10Åx10Å contoured slice centered at the viewpoint. Contouring done as lines, colors or lines & colors combined. 3-D contouring is also available as green (red for negative density) map grid points. One can also draw individual or stack of hkl planes across unit cell. |
6 | | - |
7 | | -<H3 style="color:blue;font-size:1.1em">What is plotted here?</H3> |
8 | | - |
9 | | -A drawing that shows the atoms of the crystal structure is generated. The way that the structure is displayed is determined according to the controls in this page as well as the options on the Draw Atoms page. |
10 | | - |
11 | | -<H3 style="color:blue;font-size:1.1em">What can I do with the plot?</H3> |
12 | | - |
13 | | -Use of the mouse buttons and key presses when viewing a crystal structure changes the view of the structure; see Atoms or Draw Atoms for details |
14 | | - |
15 | | -## Draw Atoms |
16 | | - |
17 | | -This gives a list of the atoms and bonds that are to be rendered as lines, van der Waals radii balls, sticks, balls & sticks, ellipsoids & sticks or polyhedra. There are four menus for this tab; Edit allows modification of the list of atoms to be rendered, Compute gives some options for geometric characterization of selected atoms, Restraints allows definition of 4 different types of restraints on the structure and Rigid body allows selection of atoms that form a previously defined rigid body. |
18 | | - |
19 | | -<H3 style="color:blue;font-size:1.1em">What can I do here?</H3> |
20 | | - |
21 | | -1. **Atom Selection from table**: select individual atoms by a left click of the mouse when pointed at the left most column (atom numbers) of the atom display; hold down the Ctrl key to add to your selection; a previously selected atom will be deselected; hold down Shift key to select from last in list selected to current selection. A selected atom will be highlighted (in grey) and the atoms will be shown in green on the plot. Selection without the Ctrl key will clear previous selections. A double left click in the (empty) upper left box will select or deselect all atoms. |
22 | | -2. **Atom Selection from drawing**: select an atom by a left click of the mouse while holding down the Shift key and pointed at the center of the displayed atom, it will turn green if successful and the corresponding entry in the table will be highlighted (in grey); any previous selections will be cleared. To add to your selection, use the right mouse button (Shift down); if a previously selection is reselected it is removed from the selection list. NB: beware of atoms that are hiding behind the one you are trying to select they may be selected inadvertently. You can rotate the structure anytime during the selection process. |
23 | | -3. **Double left click a Name, Type and Sym Op column heading**: a dialog box is shown that allows you to select all atoms with that characteristic. For example, selecting the Type column will show all the atom types; your choice will then cause all those atoms to be selected. |
24 | | -4. **Double left click a Style, Label or Color column**: a dialog box is shown that allows you to select a rendering option for all the atoms. For Color a color choice dialog is displayed that covers the entire color spectrum. Choose a color by any of the means available, press the "Add to Custom Colors", select that color in the Custom colors display and then press OK. NB: selecting Color will make all atoms have the same color and for Style "blank" means the atoms aren't rendered and thus the drawing will not show any atoms or bonds! |
25 | | -5. Menu '**Edit Figure**' - The edit menu shows operations that can be performed on your selected atoms. You must select one or more atoms before using any of the menu items. Most of these items can also be accessed by selecting one or more atoms and right-clicking the mouse. |
26 | | - * **Atom style** – select the rendering style for the selected atoms |
27 | | - * **Atom label** – select the item to be shown as a label for each atom in selection. The choices are: none, type, name or number. (NB: atom labelling slows drawing response time). |
28 | | - * **Atom color** – select the color for the atom; a color choice dialog is displayed that covers the entire color spectrum. Choose a color by any of the means available, press the "Add to Custom Colors", select that color in the Custom colors display and then press OK. |
29 | | - * **Reset atom colors** – return the atom color back to their defaults for the selected atoms. |
30 | | - * **Edit atom radii** – modify atom radii used in the bond assignment algorithm. |
31 | | - * **View point** – position the plot view point to the first atom in the selection. |
32 | | - * **Select from list** – select atoms from a popup list of names. |
33 | | - * **Add atoms** – using the selected atoms, new ones are added to the bottom of the list after applying your choice of symmetry operator and unit cell translation selected via a dialog display. Duplicate atom positions are not retained. Any anisotropic thermal displacement parameters (Uij) will be transformed as appropriate. |
34 | | - * **Add sphere of atoms** – fill in all equivalent atoms that fall within a sphere of selected radius about selected atoms. |
35 | | - * **Transform draw atoms** – apply a symmetry operator and unit cell translation to the set of selected atoms; they will be changed in place. Any anisotropic thermal displacement parameters (Uij) will be transformed as appropriate. |
36 | | - * **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. |
37 | | - * **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. |
38 | | - * **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) |
39 | | - * **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 (e.g. possible locations of missing water molecules). |
40 | | - * **Delete atoms** – clear the entire draw atom table; it is then refilled from the Atoms table. You should do this operation after any changes in the Atoms table, e.g. by a structure refinement. |
41 | | - * **Update draw atoms** – refresh the drawn atom positions from the Atoms list. |
42 | | - * **Load selected atoms** - refresh the selected drawn atom positions from the Atoms list. |
43 | | - |
44 | | -6. Menu '**Compute**' - The compute menu gives a choice of geometric calculations to be performed with the selected atoms. You must select the appropriate number of atoms for these to work and the computation is done for the atoms in selection order. |
45 | | - |
46 | | - * **View pt. dist.** - this calculates distance from view-point to all selected draw atoms; result is given on the console window. |
47 | | - * **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). |
48 | | - * **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. |
49 | | - |
50 | | -7. Menu '**Restraints**' – Individual restraints may be generated by selecting atoms and the corresponding restraint type from the menu |
51 | | - |
52 | | - * **Add bond restraint** – for selected atom pair (A-B). |
53 | | - * **Add angle restraint** – for selected atom triple (A-B-C) |
54 | | - * **Add plane restraint** – for selected 4 or more atoms |
55 | | - * **Add chiral restraint** – for selected 4 atoms; chiral atom first followed by 3 other atoms; if selected in righthand sequence, chiral volume will be > 0. |
56 | | - |
57 | | -8. Menu '**Rigid body**'/'**Define rigid body**' – assign a previously defined rigid body to selected atoms. |
58 | | - |
59 | | -<H3 style="color:blue;font-size:1.1em">What is plotted here?</H3> |
60 | | - |
61 | | -A drawing that shows the atoms of the crystal structure is generated. The atoms are displayed according to the controls in the in this page as well as options on the Draw Options page. |
62 | | - |
63 | | -<H3 style="color:blue;font-size:1.1em">What can I do with the plot?</H3> |
64 | | - |
65 | | -Use of the mouse buttons and key presses when viewing a crystal structure changes the view of the structure: |
66 | | - |
67 | | -* **Left drag**: Holding down left button rotates axes around screen x & y |
68 | | -* **Right drag**: Holding down right button translates the fractional coordinates assigned to the viewpoint (which is kept at the center of the drawing). The structure will appear to translate. The viewpoint can also be entered directly in the Draw Options. |
69 | | -* **Middle drag**: Holding down center button rotates axes around screen z (direction perpendicular to screen). |
70 | | -* **Mouse Wheel**: Rotating the scroll wheel changes "camera distance" (zoom in/out) |
71 | | -* **Shift+Left Click**: Holding down the shift key while clicking on an atom with the left mouse button causes that atom to be selected (Shift + a Right click does the same). Any previously selected atoms will be reset. If two atoms are overlapped in the current view, then the top-most atom will usually be selected. Only atoms in the asymmetric unit can be selected from the plot in this way. |
72 | | -* **Shift+Right click**: Holding down the shift key while clicking on an atom with the right mouse button causes the atom to be selected if previously unselected and unselected if previously selected. Any previously selected atoms will be continue to be selected so shift-right click can be used to add atoms to the selection list. If two atoms are overlapped in the current view, then the top-most atom will usually be selected. Only atoms in the asymmetric unit can be selected from the plot in this way. (On a Mac, control+mouse click is an alternate way to do this.) |
73 | | -* **Key n**: Pressing the "n" key selects the next atom in the displayed atom list. |
74 | | -* **Key p**: Pressing the "p" key selects the previous atom in the displayed atom list. |
75 | | -* **Key c**: Pressing the "c" key sets the plot viewpoint at unit cell center. Also resets n/p selection item to the 1st atom. |
76 | | -* **Key s**: Pressing the "s" key brings up a (large) selection of color schemes for the slice contours. Default – "RdYlGn" (Green – positive, red – negative & yellow – zero). |
77 | | -* **Key k**: Pressing the "k" key cycles through the possible slice contouring options (none, lines, colors, lines+colors) |
78 | | -* **Key m**: Pressing the "m" key for an incommensurate structure creates a movie file of the change in the structure along the 4th dimension (tau). Movie controls are found in the GSAS-II Configuration Variables. Requires the imageio python package be available for import – it is not normally available in the GSAS-II version of python. |
79 | | -* **Key +**: Pressing the "+" (or "=") key steps the viewpoint in positive drawing z-direction (toward viewer). If structure is incommensurate, "+" steps the structure and map through the 4th dimension (+tau). |
80 | | -* **Key -**: Pressing the "-" key steps the viewpoint in negative drawing z-direction (away from viewer). If structure is incommensurate, "-" steps the structure and map through the 4th dimension (-tau). |
81 | | - |
82 | 1 | ## RB Models |
83 | 2 |
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84 | 3 | There are two actions associated with rigid bodies. First the rigid body must be defined for the project, see the Rigid bodies tree item for details on that. Then the rigid body must be inserted into a phase, which is done from each phases's RB Models tab. In this process, a number of parameters are defined for each body that determine how the rigid body is placed in the cell: the location in the cell for the rigid body origin, a rotation angle and orientation vector. These can be modified while being visualized, using the mouse by holding down the Alt key. |
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