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Merge pull request #59 from Avogadro/add-template-tool
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Fix broken images
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ghutchis authored Nov 19, 2023
2 parents 3f22fea + 394d0c3 commit ca63c41
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16 changes: 8 additions & 8 deletions source/docs/tools/template-tool.md
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Expand Up @@ -58,15 +58,15 @@ As an example, we will build the salen ligand and add the attachment point for t

After creating your ligand molecule, you should select the atoms which will be the attachement sites:

![salen molecule with four selected atoms: two oxygen and two nitrogen](../../static/Ligand-SelectAtoms.png)
![salen molecule with four selected atoms: two oxygen and two nitrogen](../../_static/Ligand-SelectAtoms.png)

The Build ⇒ Add Centroid command will add a dummy atom at the center of the selected atoms:

![menu indicating "Add Centroid" command](../../static/Ligand-CentroidMenu.png)
![menu indicating "Add Centroid" command](../../_static/Ligand-CentroidMenu.png)

The ligand will now have a centroid dummy atom added. Draw bonds as desired to the attachment sites.

![salen ligand with four selected atoms and new centroid dummy atom](../../static/Ligand-AddCentroid.png)
![salen ligand with four selected atoms and new centroid dummy atom](../../_static/Ligand-AddCentroid.png)

The ligand can either be copied to the clipboard to insert via the Clipboard ligand type, or saved as CJSON to contribute to the [fragment repository](https://github.com/openchemistry/fragments)

Expand All @@ -76,22 +76,22 @@ Haptic ligands indicate bonding between a metal center and a delocalized pi syst

As an example, we will build up an η4-cyclooctatetraene ligand. Either draw the molecule or use File ⇒ Import ⇒ Download by Name… to insert the basic molecule.

![cyclooctatetraene molecule](../../static/Template-COD.png)
![cyclooctatetraene molecule](../../_static/Template-COD.png)

Now select the four atoms to use for the haptic ligand:

![cyclooctatetraene molecule indicating four selected carbon atoms](../../static/Template-COD2.png)
![cyclooctatetraene molecule indicating four selected carbon atoms](../../_static/Template-COD2.png)

Now use the "Add Centroid" command to add a dummy atom at the centroid of the selected atoms. This is useful to create distinct hapticity (e.g., η3 cyclopentadienyl after selecting three carbon atoms instead of five):

![cyclooctatetraene molecule indicating four selected carbon atoms and dummy attachment point](../../static/Template-COD3.png)
![cyclooctatetraene molecule indicating four selected carbon atoms and dummy attachment point](../../_static/Template-COD3.png)

For a haptic ligand, we need one more dummy atom, perpendicular to the pi system. We can add an additional dummy atom **perpendicular** to the centroid:

![Menu indicating "Add Perpendicular" item for haptic attachment points](../../static/Template-LigandPerpendicular.png)
![Menu indicating "Add Perpendicular" item for haptic attachment points](../../_static/Template-LigandPerpendicular.png)

After adding the perpendicular attachment, draw a bond between the centroid and the attachment site.

![](../../static/Template-COD4.png)
![](../../_static/Template-COD4.png)

You can either save this file as CJSON to contribute to the repository, or "Select None" to deselect all atoms and copy the ligand to insert into a new molecule.

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