GSAS-II provides structural visualization as part of the Phase data tree entry. This chapter introduces some of the capabilities offered there. While this can be used for publication-quality graphics and there may well be things that GSAS-II’s molecular visualization does that would be hard to duplicate in other software, it should also be noted that there are many other crystallographic graphics packages that may be better for many tasks. These include the free Mercury and Vesta programs, as well as CrystalMaker and Diamond. However, where GSAS-II’s graphics are most useful is in its integration into the structure completion and refinement process, which will be the focus of what I present here. Before going into the GUI for structure visualization, it is worthwhile to first describe what is actually displayed. For the following discussion, I will label the axes of the screen as having x horizontal, y as vertical and z as coming out from the screen.
GSAS-II uses OpenGL graphics to display the structure in three dimensions. Well, since the structure is displayed on a two dimensional screen, it is really a 2D drawing, but it includes perspective and Z-clipping (which hides objects that are too “close” to you as a viewer) and can be rotated in space, which allows our brains to interpret what we are seeing in 3D. I still find it somewhat amazing that this “3D graphics” technology, that was at first only available to me on a nearly desk-sized $60,000 Silicon Graphics computer (that a previous employer pushed me into learning to use) is now available on a mobile phone.
Dragging the mouse will change our view of the structure. Dragging the mouse up and down using the left mouse button rotates around screen x axis, and dragging right and left rotates around screen y. The middle mouse button rotates our view of the structure around the screen z axis. The right mouse button translates the view point in the plane of the screen. To move the view point in three dimensions, rotate around screen x or y and then translate again. If you have a mouse wheel, rotating that changes the “camera position”, which can be thought of as moving the structure closer or farther from where it is viewed. This can also be changed from the Draw Opts tab. The structure rotates around a point that GSAS-II calls the “view point”.
The view point is always placed in the center of the graphics window. If the “Show view point” option is set as on in the “Draw Options” tab (this is the default), it is drawn with 1 \(\mathring {\text {A}}\) lines along the a, b and c, directions, with the lines colored red, green and blue, respectively. The unit cell, when outlined, is also drawn with red, green and blue lines for the a, b and c, axes, respectively. Colored lines are used for the lines starting from x=y=z=0 and the remaining lines are white.
To provide some orientation to the GUI, there are three tabs within each phase data tree entry that all interact for visualization; they are the “Atoms“, “Draw Atoms” and “Draw Options,” which will be discussed further in this chapter, but there are other tabs that can also influence what appears in the visualization. Here is a synopsis of all these phase tabs and their relevance to structure visualization: