Custom Model Creator
Definitions
Bead ID: Identifier used by the algorithm to generate the coarse-grained structure and define connectivity between beads.
Bead Name: The label displayed in the Mol* viewer for visualization purposes.
Rules of creating custom beads
To define a bead that covers multiple residue types, create multiple entries manually and assign them the same Bead ID.
-
For A, G, C, U: Add 4 separate beads (select scope A, G, C, U respectively) and give them all ID e.g.,
A2. -
For Purines/Pyrimidines: Add 2 beads with the same ID (e.g.,
A3). -
Defining a link for one bead (e.g.,
A2) will automatically apply to all other beads with the same ID.
Beads List
Direct mapping allows 1 atom.
Select at least one atom.
Intra-Residue Connectivity
Click intersections to connect beads within a single residue.
Only upper triangle is active to prevent duplicates.
Inter-Residue Connectivity
Define connection between Residue (i) and Residue (i+1). Max 1 connection allowed.
No inter-residue connection defined yet.