Designing a polymer from molecular fragments can become tedious when the chain contains more than one building block. You need to keep track of which fragments connect, how often they repeat, and whether a connection should be single, double, or triple. Polymer Builder in SAMSON brings those decisions into one workflow: register fragments as monomers, combine them into reusable sequences, and describe the final chain with a compact expression.
The key is to treat connection points as part of the design—not as an afterthought. Before building a long chain, check that each fragment has suitable start and end atoms. Polymer Builder automatically selects atoms at opposite ends of a selected fragment, and you can override those choices using the selection or atom-picking controls. This makes the connection direction explicit and helps you inspect the building blocks before assembling them.
Prepare reusable building blocks
Start by opening Polymer Builder from Home > Apps > Assembly > Polymer Builder. Select a molecular fragment in the document or viewport, then choose Register monomer from selection. The app assigns each registered monomer a unique letter, such as A or B. The table also reports approximate molecular weight and the distance between the selected start and end atoms, useful checks when comparing candidate fragments.
If the automatically chosen connection atoms are not the ones you intend to use, set them explicitly: select a single atom and use the selection control, or pick an atom from the structure’s atom list. You can highlight a monomer to confirm which structure it refers to. If you modify a registered fragment in SAMSON—for example, by adding or removing an atom—it is deregistered, so make structural edits before relying on it in a final build.
Capture patterns once, reuse them in the chain
For a repeating pattern, register a sequence instead of typing the same monomer pattern repeatedly. Click Add new sequence and enter registered monomer IDs, such as ABBA. Sequences receive identifiers such as S1 and S2, which can then be used in the final expression. A sequence can be highlighted for a quick visual check, and its status indicates whether the expression is valid.
Connections default to single bonds. To specify other bond types between monomers in a sequence, use = for a double bond and # for a triple bond: A=B or A#B. The sequence table provides approximate molecular weights and lengths, so you can compare patterns before using them in a larger chain. If you want the monomers of a sequence grouped under a common parent in the generated structure, provide a name in the sequence’s Name property.
Describe the polymer, then inspect the result
The final expression combines monomer IDs, sequence IDs, and repeat counts. For example, 2*AB means two repeats of AB, producing ABAB. Likewise, 2*S1 + 2*S2 joins two repeats of each registered sequence. You can also specify a bond between expression components: AB=BA connects those components with a double bond, while AB#BA uses a triple bond. Predicted molecular weight and length are shown before you generate the polymer.
These predictions are helpful for planning, but the generated structure still deserves a visual check. The polymer’s shape is based on the directions between each monomer’s start and end atoms. At connection sites, excess hydrogens are removed. The advanced options can adjust hydrogens on connection atoms based on valence and try to avoid steric overlaps; clash adjustment may introduce slight curvature. If the structure needs further refinement, SAMSON’s built-in minimizer is available under Edit > Minimize.
A useful habit is to save the full project when you want to preserve your registered monomers and sequences, and save the selected polymer separately when you need an exported structure. You can also use a generated polymer as a monomer for a larger construction, such as a block copolymer or extended chain.
For the complete interface walkthrough, see the Polymer Builder documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.