Merging Structures

MarvinSketch allows you to merge two already drawn molecules in a few steps.

As the merging points in both the template and the substituent molecules (1, 2 or 3 pairs of them) is assigned, the template coordinates do not change, only the substituent is resized, rotated (in three dimensions) and moved to fit the template.

  1. Select images/download/attachments/48075924/merging_mapper_tool24.png Assign Atoms from the Structure < Directed Merge submenu or from the 3D Editing toolbar.

  2. Click and drag the arrow from the atom of the substituent to the template molecule. The arrow will be numbered.

  3. Repeat the process (the Assign Atoms action is still active, no need to re-select the command) once ore twice to define more merging points.

  4. Merge the molecules by selecting the images/download/attachments/48075924/directed_merge_in_3d24.png Merge command from the Structure > Directed Merge submenu or from the 3D Editing toolbar.

In case of assigning 1 or 2 atom pairs, the subsituent is selected after the merge and the Rotate mode is active, and you can rotate the substituent around an axis:

1 atompair To finish merging, click anywhere on the blank canvas.

  • one bond - the bond is the axis;

  • two bonds - the axis is the bisector of the angle of these bonds;

  • 3 bonds choose the x,y, or z axis, or define the axis by selecting two atoms.

2 atompairs

  • The rotation axis is defined by the two connection points of the template and the substituent. Upon clicking on images/download/attachments/48075924/directed_merge_in_3d24.png Merge the mouse gets in Rotation mode and the user can rotate the substituent till the desired position.

  • If any atom pairs fall in the merging range after the rotation, they will be merged.

If this second merge happens only on one atom pair, the substituent remains selected, and is subject to a second rotation action, where the rotation axis is defined by the original and the new connection points.

How to merge structures


Assigned atoms

Selected for rotation

Merge product

1 atom pair




2 atom pairs




3 atom pairs