Lock Atom(s): If you want to prevent a certain node from allowing substitution, use the Lock Atoms tool. A box will appear around the atom that you have locked.
Lock Ring Fusion/Formation: The ring will be bold once it's had the ring fusion applied to it.
Note: This does not mean that substitution is blocked, it means that no further rings can be fused to an already existing one.
Last updated 9/12/2025
The images above come from the SciFinder Help
The video above details how to assign fragments to an R-group. Fragments are only one of the options when assigning R-groups, you can also assign Atoms, Variables, Shortcuts, or a combination of these as an R-group. Up to 20 R-groups can be used in a structure, but be careful, this may be too complex to complete in SciFinder.
Last updated 9/12/2025
The Variable Attachment tool is used to specify variable positions for a substituent to attach on a ring system. No more than 20 total substituents can be attached to a single ring system.
The substituent atom cannot attach to more than one ring system, though a structure can have more than one VPA if desired. The substituent must be a single atom or an atom in a larger fragment, and it cannot be part of a repeating group.
The attachment atom can be a single atom or an atom in a larger fragment, but it cannot be a shortcut, a metal atom, of the M, Ak, Cb, Cy, or Hy variables. It also cannot be part of a repeating group.
See the video below for an example of how to use the VPA tool:
Last updated 9/12/2025 using information from here.
To use pre-drawn or custom templates, select the following icon in the left-side menu of the structure editor:
You can find pre-drawn templates for the following groups:
Alkaloid Amino Acid Bicarbocyclic Carbohydrate Coordination
Cycloalkane Miscellaneous Monocarbocyclic N-containing NOS-containing
Nucleic Acid O-containing Polycarbocyclic S-containing Steroid
You also have the ability to save your own template, which can come in handy if you are often drawing substances with similar cores or even drawing the same substance, you can navigate to your templates and easily paste into the structure editor.
You can either upload a .cxf file into My Templates:
Or you can save a template from the structure editor. Once you have drawn a structure, select the 'Save As Template' button and enter a name for your template:
Last updated 9/11/2025
