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Diamond - How to colorize organic linkers using Copy Style and Paste Style

Diamond can deposit multiple styles of different objects using the command Copy Style from the Edit menu and transfer ("paste") it to multiple other objects using the Paste Style command.

This article shows how to colorize all atoms of a special molecular fragment including its connecting bonds. This is to emphasize an organic linker in a metal-organic framework (MOF)., here: terephtalic acid.

Note: This requires Diamond version 5.1 or higher.

You can find the sample files here:
COD-1516287-MOF-5-280-K.cif
COD-1516287-MOF-5-280-K.diamdoc
COD-1516287-MOF-5-280-K-sky-blue-terephtalate.diamdoc

Note: This article is in preparation. This draft outlines the approach:

  1. Locate one terephtalic acid fragment in the structure picture (the 8 C atoms by default use light grey color, the 4 H atoms white, and the 4 O atoms red; the 16 bonds are yellow by default).
  2. Select the 16 atoms of the terephtalic acid unit (by clicking or by capturing them with rectangular selection).
  3. Use the new command Select Bonds of Fragment, added in version 5.1 to Diamond (Edit/Extended Selection sub-menu).
  4. Run the command Display/Atom Designs and choose to edit the designs of the 16 atom (rather than the atom group and sites designs).
  5. In the Atom Design dialog change the fill color (this button is indeterminate because the 16 atoms use different fill colors) to light blue and confirm with OK.
  6. Repeat this for the 16 bonds using Display/Bond and Contact Designs (choose for the 16 bonds) and change the bond fill color to light blue, too.
  7. Now that the 16 selected atoms and 16 selected bonds are all light blue, run Copy Style. This will show you a small popup window that one atom design and one bond design have been deposited (for use with Paste Style).
  8. Use the new command Select Symmetry-Related to mark all atoms and bonds of the remaining terephtalic acid units in the picture that are symmetry-related to the currently selected one as selected.
  9. Use the Paste Style command to turn all C, H, and O atoms including the bonds between of all terephtalic acid units in the picture to light blue. The oxygen atom in the center of the inorganic building unit remains red, and the polyhedra remain unchanged, too.