Create a bond

Bonds are displayed as lines connecting monomers and sequences. Different colourings are used for backbone (black), side-chain (orange) and every other (pink) types of bonds to distinguish the interaction.

These bonds can represent chemically exact bonds between specific atoms of specific monomers, or ambiguous bonds, which are more vaguely defined.

Exact interactions are displayed by bonds connecting the two monomer shapes directly, while ambiguous interactions are shown by bonds between a component rectangle's edge and a monomer shape.

images/download/attachments/1806409/example_peptide_bonds.png

Ambiguity types supported by BioEddie:

  • Bonds to BLOBs, which do not exhibit a chemical structure definition

  • Bond position ambiguity (?:R and [abbreviation]:R)

  • Attachment point ambiguity (R?)

Create a defined bond

Exact bonds between PEPTIDE, RNA, CHEM monomers can be created involving known attachment points.

To create a defined bond

  1. Click on the bond drawing images/download/thumbnails/1806409/bond_drawing.png button.

  2. Hover over the starting monomer.

  3. Click on it, then drag the cursor to the other monomer, and release the mouse button. M onomers without free attachment points are greyed out.

  4. If at least one of the involved monomers has more than one free attachment point, the 'Create bond' dialogue will open where you can select the intended attachment point.

  5. The bond is created and visualised by a line connecting both monomers.

Note that bonds to BLOBS are ambiguous and visually the same style as defined bonds

images/download/thumbnails/1806409/exact_bond.png

Create an ambiguous bond

Ambiguous bond can be created where at least one side of the bond does not target an exact attachment point of a specific monomer, i.e. an entire sequence, a specific monomer type inside a sequence, or a BLOB monomer.

To create an ambiguous bond

  1. Click on the bond drawing images/download/thumbnails/1806409/bond_drawing.png button.

  2. Hover over the starting canvas element.

  3. Click on it, then drag the cursor to the other canvas element e.g. a sequence, and release the mouse.

  4. The 'Create bond' dialogue appears where you further refine the bond definition.

  5. The bond is created and visualized by a line connecting both canvas elements.

images/download/attachments/1806409/ambiguous_bond.png