Is there a way to build with fragments that aren't in the Fragments tab of the Build panel?
If you want to build a molecule with fragments that aren't in the Fragments tab, here are some options:
- Use a fragment that has a similar structure, then change the atom types. For example, if you wanted to add a cyano group, you could instead add an alkyne group, then change the CH carbon to a N, using the Set element button on the Build toolbar. The terminal H should be automatically deleted (provided you have the option "Adjust number of hydrogens following build operations" selected in the Builder section of the Preferences panel).
Use the Draw tool to draw the new group. You can draw the heavy-atom framework as a carbon skeleton, add multiple bonds as needed, and then change the carbon atoms to other elements as needed. When you have done this, add hydrogens and do a geometry cleanup to relax the geometry.
Add custom fragments to the Fragments tab. See KB article 1031 for more information.
Maestro, build, custom fragments
#1031: How do I add fragments to the Build panel fragment library?
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