You should see a repetition of the Mg atoms along the a-axis. This is good when you are working with an extended plot range (i.e., several unit cells), and wish to tidy up your display so that you can see the proverbial wood for the trees. Orient the stucture so that you are looking down the c-axis. The Hide Molecular Fragments command searches through the bonding specifications and hides any molecules which are incomplete. Hiding Molecular FragmentsĪn alternative to repairing molecular fragments is simply to hide them. You can "repair" these molecular fragments with the Repair Molecular Fragments command: the program generates additional atoms so that all atoms in the original view are now part of intact molecules. If you have chosen an arbitrary view of part of a crystal, (e.g., by using the Set Range command), some of your molecules may well have been truncated - this happens when they straddle the plot range. (Note that, in order to ensure that all molecules are intact, some atoms may straddle the unit cell boundary other atoms that lie within the unit cell may be hidden, to ensure that only one unit cell's worth of crystal is shown.) Repairing Molecular Fragments This command is a great starting point for working with a molecular crystal: you get the complete unit cell contents - and they are all intact molecules! The Show Molecular Cell command calculates the best arrangement of (fully-intact) molecules to be displayed, corresponding to a complete unit cell's contents. If this is the case, please use the Elements pane of the Preferences window, and choose a more appropriate element table (e.g., the CSD CrystalMaker Covalent Radii), which you can then apply to an existing structure (remembering to edit your bond specifications afterwards) and Save as your default set for later use.
CrystalMaker's default element table is set up for inorganic structures, and you may find that C-C and other common bond distances are too small. This is especially a problem if you tend to use organic structures. Insight into crystal structures, including some complex silicates, is aided by the use of the CrystalMaker computer program. It is crucial that you check your bond specifications, before proceding to use one of the Optimize Range commands, otherwise you may find "incomplete" molecules are displayed.Ī common mistake is to use the wrong Element Table at the outset, so that bond specifications use inappropriate atomic radii, with the result that not all bond linkages are created.
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