Building a polymer model often starts with a collection of fragments and a deceptively difficult question: how do you connect them in the right order without rebuilding every chain by hand? A useful approach is to treat fragments as reusable monomers, save recurring patterns as sequences, and then describe the final chain with a compact expression. Polymer Builder in SAMSON brings those steps into one workflow.
This is especially helpful when comparing chain designs, assembling repeating blocks, or preparing a structure for later modeling. The key is to prepare the connection points carefully: the software uses each monomer’s start and end atoms to orient and connect the fragments.
1. Register fragments with clear connection points
Open Polymer Builder from Home > Apps > Assembly > Polymer Builder, or find it using SAMSON’s Find everything… search. Select a candidate monomer in the Document view or Viewport, then choose Register monomer from selection. The app assigns each registered monomer a unique letter, such as A or B.
Polymer Builder automatically selects start and end atoms at opposite ends of a fragment. Since those atoms determine how units connect, inspect the choices rather than assuming the automatic selection matches your intended chemistry. To change a connection atom, select one atom and use S, or use P to choose an atom from a list. The V control can highlight the structure or atoms to help you check what is selected.
The monomer table displays molecular weight and the distance between its start and end atoms. These values provide a practical way to compare registered fragments before building a long chain. If you edit a monomer’s structure in SAMSON—for example, by adding or removing an atom—it is deregistered from the list, so check the table if an expected unit is missing.
2. Save repeating patterns as sequences
If a design contains a block you expect to reuse, register it as a sequence instead of typing its individual monomers repeatedly. Choose Add new sequence and enter the monomer IDs, such as ABBA. Sequences receive identifiers such as S1 and S2, which can then be used in the final expression. The V button highlights the monomers in a sequence, making it easier to verify that the pattern contains the intended units.
Check the sequence’s Status property: an incorrect sequence displays an error, while a valid one is marked Valid. You can also give a sequence a name if you want its monomers grouped under a common parent structural group in the generated polymer.
3. Write the chain as an expression
The final expression can combine monomer IDs, saved sequence IDs, repeats, and different bond types. For example, 2*AB means two repeats of the pattern, producing ABAB. Likewise, 2*S1 + 2*S2 specifies two repeats of each saved sequence. The plus sign separates components in the expression; use the examples shown by the app’s format when composing a design.
Connections default to single bonds. Use = for a double bond and # for a triple bond: A=B connects A and B with a double bond, while A#B uses a triple bond. These symbols can also appear in a larger expression, such as AB=BA. Before generating, review the monomer order, repeat counts, and any non-single bonds—the expression is a concise specification, so a small typo can change the chain you intend to build.
Polymer Builder shows predicted molecular weight and length below the expression. Treat these as planning estimates, then generate the structure and inspect the result. The generated shape is based on the directions between each monomer’s start and end atoms, and excess hydrogens at connection sites are removed.
4. Inspect connections and prepare the structure
Two options can help with connection-site geometry. Adjust Hydrogens on connection atoms adjusts hydrogen counts and positions at the start and end atoms based on valence. Adjust for clashes tries to avoid steric overlaps when connecting units; this may introduce slight curvature. These settings address different concerns, so consider the chemistry and geometry of your fragments when deciding how to build the chain.
After generation, inspect the structure before using it downstream. If needed, SAMSON’s built-in minimizer is available through Edit > Minimize; it uses the Universal Force Field. You can save the selected polymer with Home > File > Save selection as…, or save the full project to preserve the monomer and sequence tables for later work. A generated polymer can also be reused as a monomer when building block copolymers or longer chains.
This workflow turns a collection of fragments into a reusable construction kit: define connection atoms, validate patterns, express the chain, then inspect the generated geometry. For the complete instructions and interface details, see the Polymer Builder tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.