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Article ID: 700 - Last Modified: October 19, 2012

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.

Keywords: Maestro, build, custom fragments

Related Articles:

#1031: How do I add fragments to the Build panel fragment library?

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