The 3D Alignment Plugin overlays molecules onto each other by translating and rotating them in the space. The molecules shoud be pasted on to the same MarvinSketch canvas by reading multiple molecules from a file. You can also copy & paste or drag molecules from another sketch panel.
The input can be two or more molecules in 2D or in 3D. If 2D molecules are given, their 3D structure is automatically generated.The molecules can be treated rigid (then the original conformation is preserved), or flexible (then dihedral degrees of freedom are added to the molecule). To preserve the input conformation simply select the molecule on the canvas.
The output is the ensemble of aligned molecules in displayed in a MarvinSpace canvas. The input and output molecules are all displayed in different colours and shown in a tree view on the right side of the canvas. To save the aligned orientation use the popup menu and click on the molecules with the right mouse button.
Fig. 1 Input and output molecules displayed on the result MarvinSpace canvas
Following options can be set in the 3D Alignment Options panel:
Display in MarvinSpace: if ticked, the result window is a MarvinSpace 3D viewer. Molecules are visualized in different colours for better distinction of structures.
Fig. 2 Alignment Options panel
Let's suppose you have an SDfile contaning some molecules (called wish.sdf) that you wish to align. This must be converted for the alignment to a single molecule multi-fragment file where each fragment is a molecule from wish.sdf:
Type at command prompt:
If you know which atoms to overlap use the Reaction arrow tool to connect them. This can improve the alignment. If you have only 3D molecules as input and you select one of them, its original conformation will be preserved during the alignment, while others remain flexible.