![]() ![]() Placing a Fragment in a Centroid Position The green pushed-in tack indicates that the palette is “tacked” to the desktop (i.e., “sticky”): the red upward pointing tack similarly indicates modal operation. The thumbtack icon in the upper left corner of the window shows whether the palette will close when another one is selected (or a non-building context is entered). The various palettes in GaussView can be used in a modal (dialog box behavior) or amodal (floating palette behavior) manner. When the Type field is set to Nucleoside, the left popup menu below the Type field can be used to select the desired DNA base (nucleic acid fragment), and the right popup menu in that line allows you to specify the structural form as Central Fragment, C3’-Terminal Fragment, C5’-Terminal Fragment or Free Nucleoside. When Amino Acid is selected, the left popup menu below the Type field can be used to select the desired amino acid, and the right popup menu in that line allows you to specify the structural form as Central Fragment, Amino-Terminal Fragment or Carboxyl-Terminal Fragment (the last two are the N-terminated and C-terminated forms, respectively). The Type field allows you to select either Amino Acid or Nucleoside. Use the various fields in this window to select amino acids and DNA bases. The default biological fragment is Alanine Central Residue.įigure 14. The Biological Fragments palette presents a set of AM1-preoptimized fragments useful to biological researchers: the amino acids and various DNA bases (see Figure 13). Use this palette to select the desired ring system. The Ring Fragments window allows you to select from a series of AM1-optimized ring structures. These fragments include a five-member ring with an open bond perpendicular to the plane of the ring: a n5-cyclopentadienyl ligand for use in constructing organometallic systems (circled in Figure 12). Note that several of the fragments use non-traditional bonding. Use this palette to select the desired functional group. The default group is carbonyl (formaldehyde). The R-Group Fragments window allows you to select from a series of AM1-optimized functional group fragments. In this case, the current atom type is pentavalent sulfur. The available hybridization (connectivity) variations for the selected element appear along the bottom of the palette. The default element type is tetrahedral carbon. The various possible coordination patterns for the selected element are shown at the bottom of the window (see Figure 11). The Element Fragments palette allows you to select an element from the periodic table. Note that the standalone Builder palette is opened with the View=>Builder menu item and can be made to always stay on top of all other open windows by checking the Builder Dialog Stays on Top checkbox in the Window Behavior Preferences (accessed with the File=>Preferences menu path). Clicking on either the Active Fragment area on the standalone Builder palette or on the fragment name above the main window’s Current Fragment area opens the palette corresponding to the selected fragment type. The current item always appears in the Current Fragment area of the GaussView control window and/or the Active Fragment area of the standalone Builder palette (see Figure 3). The desired atom or fragment is chosen using one of the Element, Functional Groups, Rings and Biological Fragments buttons and then selecting one of the choices from the resulting palette. ![]() ![]() Clicking on an existing atom adds the current item to the existing structure at the indicated point, usually replacing it (other options are discussed later). Clicking in an open area of the View window adds the current atom or fragment to the window as a distinct fragment. In general, GaussView begins and remains in its insert/replace mode, unless one of the options described below explicitly calls for it to act in a different manner. The GaussView molecule building tools always operate on the active View window. See the next major section of this manual, “Opening, Displaying and Saving Molecules and Views,” for information on using GaussView view features and opening and saving molecule files and images. These options enable you not only to construct new structures either atom-by-atom or from fragments, but also to manipulate and examine previously-computed molecules. This section describes GaussView’s molecule building features. ![]()
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