diff --git a/source/docs/tools/template-tool.md b/source/docs/tools/template-tool.md index f27b7acd..e5176ee4 100644 --- a/source/docs/tools/template-tool.md +++ b/source/docs/tools/template-tool.md @@ -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) @@ -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.