Groups-Link Nodes

Marvin JS does not differentiate between SRU, Repeating units, Link nodes, and Copolymers in display or creation.

However, there are restrictions to export a group as a Link node, these are as follows:

  • There must be one atom in the group.

  • The repeating pattern must not have been set (or it must be the default value).

  • The number of repetitions must be a range that starts at 1.

Create a Link Node

With the S-group Tool

  1. Select the S-group tool , then select the atom you would like to change to a link node with it.

  2. Then the S-group Dialog opens. Leave the repetition pattern on the default value and set the repetition range from the value 1 to the number you would like, then click OK.

  3. After the dialog closes, the link node is established.

images/download/attachments/1803040/Creating_a_Link_Node_1.png

With Selection

  1. Select the atom you would like to group with one of the Selection tools then click the S-group tool.

  2. The S-group Dialog opens. Leave the repetition pattern the default value and set the range from the value 1 to the number you would like, then click OK.

  3. After the dialog closes, the repetition unit has been established.

images/download/attachments/1803040/Creating_a_Link_Node_2.png

Modifying a Link Node

You can change a Link node to a Repeating unit an SRU by changing the range, or the repeating pattern.

Changing the atom type, in this case, is not possible.

Deleting a Link Node

Right-click on the atom in the brackets, then select Ungroup from the menu.

When you modify the atoms or bonds in the group, it will automatically ungroup.