Building a polymer model from individual molecular fragments can become tedious quickly. You need to keep track of which units connect, how often they repeat, and whether a connection should be single, double, or triple. If you also need to reuse the same building blocks in different designs, starting over for each chain is an unnecessary source of mistakes.
SAMSON’s Polymer Builder offers a practical workflow: register molecular fragments as monomers, save recurring patterns as sequences, then describe the polymer you want with a compact expression. This is useful for exploring a family of candidate structures without manually assembling every copy of every fragment.
Start with connection-ready fragments
Before opening the app, place the candidate monomer fragments in your SAMSON document. Launch Polymer Builder from Home > Apps > Assembly > Polymer Builder, or find it using Find everything… with Shift+E.
Select a fragment and choose Register monomer from selection. Polymer Builder assigns each registered monomer a unique letter, such as A or B. It automatically identifies start and end atoms at opposite ends of the fragment. These atoms determine where the units will connect, so check them rather than treating registration as a purely administrative step. If needed, set an atom from your current single-atom selection with S, or pick an atom from the structure using P. The V control can highlight the relevant structure or atoms.
The monomer table shows molecular weight and the distance between its start and end atoms. These values provide a useful quick check that the intended fragment was registered. You can also edit entries in the table. If the structure of a registered monomer is later changed—for example, by adding or removing an atom—it is deregistered from the list, so register it again after making such edits.
Save repeating patterns once
When a polymer contains a recurring block, register that pattern as a sequence instead of repeatedly writing out its monomers. Click Add new sequence and enter the monomer IDs—for example, ABBA. Sequences receive identifiers such as S1 and S2, which can then be used in the final expression. The status indicates whether a sequence is valid; if it is not, check that its monomer identifiers are registered and spelled correctly. Use the sequence’s V button to highlight the monomers it contains.
Connections are single by default. Put = between units for a double bond, or # for a triple bond: A=B and A#B are simple examples. A sequence can also have a name if you want its monomers grouped under a common parent structural group in the generated polymer.
Describe the chain, then inspect the result
The polymer expression combines monomers, saved sequences, and repeat counts. For example, 2*AB represents ABAB, while 2*S1 + 2*S2 repeats each of two registered sequences twice. You can also specify bond types in an expression: AB=BA connects AB and BA with a double bond, and AB#BA uses a triple bond. The predicted molecular weight and length shown by the app are estimates to review before generating the structure.
Click Generate polymer when the expression is ready. The generated shape is based on the directions between the start and end atoms of each monomer, and excess hydrogens at connection sites are removed. The advanced options let you adjust hydrogens at connection atoms based on valence and try to avoid clashes; clash adjustment may introduce slight curvature. These controls affect how the model is built, so inspect the generated structure rather than assuming the expression alone determines its final geometry.
If you need to refine the structure, SAMSON’s built-in minimizer is available under Edit > Minimize; it uses the Universal Force Field. You can save the selected polymer using 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 registered as a new monomer when building block copolymers or extending a chain.
This workflow helps separate three common tasks—choosing connection points, defining reusable building blocks, and specifying the overall chain—so an edit to the sequence does not require rebuilding the model unit by unit. For the complete tutorial and interface details, read the Polymer Builder documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.