18.2 Phase “Draw Atoms” tab

The information shown on the Draw Atoms tab is a list of atoms that may include symmetry replicants of atoms in the Atoms tab. There is an extensive list of menu commands that determine how atoms are added to this list, as will be discussed further below. Note that the only settings that can be changed for each atom in this list are entries in the columns labeled Style, Label, and Color. Note that these settings are independent. The values for these settings can be changed one at a time, by clicking on the appropriate box in that column, or you can use the “Atom style”, “Atom label”, and/or “Atom color” menu commands in the “Edit Figure” menu. This will change the value for all selected atoms, or, if no atoms are selected, you will be given a window to select atoms. Also, it is possible to change the values for one or more atoms by selecting them and using a right click, or by double-clicking on the column label.

18.2.1 Atom selection

Atoms may be selected in the table by clicking on the row label (to the left). If the shift key is help down, ranges of atoms can be selected and if the alt key (cmd on Mac) is held down, individual atoms can be added or removed from the selection list. Alternately, the “Edit Figure”/“Select from list” menu command can be used and you will be given a window to select atoms. Finally, with the plot window active, one can advance the selection through the Draw Atoms atoms table by pressing on the “n” or “p” keys. Note that when atoms are selected in the table, their color is changed to a bright green. This can be helpful when trying to understand the structure difference between the crystallographically different atoms with the same element type. When the “n” or “p” keys are used for selection, the view point will be placed on that atom.

18.2.2 Style options

The style setting dictates how atoms are displayed. The options are:

• lines: Here thin lines are used to connect atoms. If an atom has no bonds, it will not be directly visible.
• vdW balls: This draws the atoms as van der Waals spheres that are intended to be space-filling. Bonds are not drawn to connect atoms that are drawn as van der Waals spheres. There is a scaling factor for the size used for van der Waals spheres that can be adjusted on the Draw Options tab.
• sticks: Like the lines mode, atom positions are not drawn directly, but bonds between atoms are shown. However, in this mode, cylinders are used to show bonds. The thickness of the cylinder can be adjusted on the Draw Options tab.
• balls & sticks: This places spheres at the positions of selected atoms and also draws bonds as cylinders between atoms. The same adjustment on the Draw Options tab for the thickness of the “sticks” cylinders also changes the bonds here, but there is a separate scaling factor for the ball size on the Draw Options tab.
• ellipsoids: This option will draw atom sizes as proportional to the APD values. Ellipsoids are used for atoms where anisotropic \(\rm U_{ij}\) values are refined and spheres are used where \(\rm U_{iso}\) is selected. There is an ellipsoid probability factor on the Draw Options tab.
• polyhedra: This option draws solids around bonded atoms, The color of the solid is determined by the central atom.

18.2.3 Label options

Labels can be placed at atom positions, but these labels may be hidden by spheres or ellipsoids if one of these options has been selected. Dropping the scaling/probability factor down will reveal the labels. The choices for label are:

• type, where the label is the element type,
• name, where the label is the name specified for the atom on the“Atoms” tab.
• number, where the number listed by the sequence on the“Draw Atoms” tab. Note that this and atom selection are the ways to distinguish between symmetry replicants of atoms.

If the label option is left blank (the default), no label is provided for that atom.

18.2.4 Atom colors

The default atom color is set from the value for the element type shown on the General tab. The default can be changed there. When any of the methods given in §18.2 is used, a dialog will be presented for color selection, but the nature of this dialog will be determined by the operating system on your computer.

18.2.5 Adding to the Draw Atoms

When the Draw Atoms tab is first selected, the atoms in the asymmetric unit, as listed on the Atoms tab, are placed into this list. If all the atoms are deleted from the Draw Atoms list, the contents are reset to the atoms in the asymmetric unit. There are a number of commands provided that allow you to expand the number of atoms in the Draw Atoms list. Note that they will all remove duplicate atoms, so you do not need to worry about an operation that will duplicate atoms that are already in the list.

• Fill unit cell: The menu command that I use more than any other is “Fill unit cell”. This will take the selected atoms (or ask if none are selected) and find all the symmetry replicants of those selected atoms that are located in the unit cell and add them to the Draw Atoms list.
• Fill CN-sphere: This will add the atoms directly bonded to the selected atoms.
• Add sphere of atoms: Here one designates one or more “origin” atoms and a sphere of a specified radius is searched for atoms that are within that distance. You can select what type of atoms will be searched.
• Add atoms: This command allows one to apply a specified symmetry transformation to a set of atoms. Note that the selected symmetry operation is applied directly to the position of the atom as it appears in the Draw Atoms listing. A good way to generate two unit cells worth of atoms is to first use the “Fill unit cell” menu command and then select all atoms in the table and use the “Add atoms” command. Here use the X, Y, Z symmetry operator and do not force to unit cell and then select the a neighboring unit cell [(1,0,0) or (0,1,0) or (0,0,1) or (-1,0,0) or (0,-1,0) or (0,0,-1)]. Repeat the “Add atoms” command to expand further. While I cannot provide examples, I am sure there are many other ways this command could be used to create useful sets of atoms to plot.
• Transform atoms: This command works very similarly to the “Add atoms” command except that instead of adding the generated positions, the existing atoms in the Draw Atoms list are replaced by the generated positions. If you have an asymmetric unit that has atoms outside the unit cell, but want to obtain the unit cell contents, use this command with the option “Force to unit cell” set as “yes,” either before or after the “Fill unit cell” menu command.
• Complete molecule: This is most useful for structures with discrete molecules, rather than structures that create infinite networks, but sometimes can be useful for the latter by not including linking atoms (for example metal ions in MOFs). What it does is use the “Fill CN-sphere” command on the selected atoms and then applies the “Fill CN-sphere” command on the atoms that have been generated. This command will fill out the bonding in molecular fragments and then stop once all the atoms in the fragment have been located. If accidentally launched on an infinite framework, it will keep discovering new bonded and would never stop, which is why the command has a limit for how many iterations will be applied in the command and the maximum number of atoms that will be allowed.

18.2.6 Other Actions from Draw Atoms

Here are some of the other actions that can be performed from the Draw Atoms tab from the “Edit Figure” menu:

• Set view point: the view point is set to the average position of the selected atoms. Works nicely with a single atom or a group of atoms.
• Update draw atoms: Usually the information in the Draw Atoms list is synchronized to changes in the Atoms list, but should that fail, this command will update the Draw Atoms coordinates/ADP values.
• Load selected atoms: This can be used to copy selected atoms from the Atoms list to the Draw Atoms list. This is not commonly needed, but might be used after an atom is accidentally deleted from the Draw Atoms list or has been transformed, but is wanted at the original position again.
• Randomized Action: This selects atoms in a randomized order and gives you the opportunity to do something you have chosen to those selected atoms. As an example, if you want to convert a structure that has vacancies noted by partial occupancy to an atomistic model, you might want to delete a percentage of those atoms. With this command, you could select all the generated symmetry replicants of that atom and then delete the first n% of those atoms.

This action can be performed from the Draw Atoms tab from the “Compute” menu:

• Create void map: this sweeps through the unit cell on the specified grid spacing and locates points where there are no atoms (as determined by their space-filling radius) within a specified distance. Blue dots (actually small cubes) are then placed at those locations where there are no atoms. The default is to create small blue dots that can be somewhat hard to see against a black background on some monitors, but the GUI allows them to be made brighter or to change the size or color.

18.2.7 Window keystrokes

These commands require that the plot window be active (by clicking on the graphics window border or inside the window).

• c: pressing the “c” key will reset the view point to its default value of (\(\frac 12, \frac 12, \frac 12\)).
• n: will select the next atom in the Draw Atoms list
• p: will select the previous atom in the Draw Atoms list
• +: The “+” key the view point along the screen z-axis, moving the view point in the direction towards the viewer, The structure will appear to move away as the plot is centered on the new view point.
• -: The “-” key moves the view point along the screen z-axis, moving the view point in the direction away the viewer, The structure will appear to towards the viewer.