Working with complex molecular systems often starts with a simple question: how do I select only what I need? Whether it’s isolating ligands, ions, or protein residues, efficient selection is one of the key steps in molecular modeling workflows — such as preparation, analysis, or visualization. In SAMSON, the integrative molecular design platform, the Select menu provides an extensive set of capabilities to make this process easier and faster.
Let’s take a look at how SAMSON helps you go from juggling countless atoms to focusing only on the ones that matter — all through intuitive yet powerful selection tools.
Two Paths: Operations and Structures
The Select menu in SAMSON is organized into logical groups:
- Operations: These allow you to find, expand, or reduce selections based on relationships — such as parents, descendants, connected atoms, or similarity.
- Structures: Use these to select molecular components based on biological or chemical classification, like chains, residues, atoms, bonds, or water molecules.
Selection Strategies That Make a Difference
A few practical examples can help illustrate how SAMSON supports different selection needs:
1. Selecting a Binding Site
Need to dock a ligand but don’t want to simulate the entire protein? Simply go to Select > Structures > Biology and choose the binding site or a specific chain. This lets you focus your simulation or minimization only on relevant atoms.
2. Cleaning Water Molecules
Water often floods PDB files. To eliminate them, just use Select > Structures > Water, then delete or hide.
3. Manual Targeting with Selection Filters
Each selection editor — such as Rectangle or Point selection — also respects selection filters located in the top-right corner of the viewport. Need to select only residues, and not atoms? Toggle what gets included in your selections using this filter.
4. From a Single Atom to a Full Chain
With one atom selected, you can expand upward: use Select > Operations > Parent to climb the hierarchy (e.g., to residue or chain). Similarly, use Descendants to go from a residue to all the atoms it contains.
5. Intelligent Grouping
Once you’ve pinned down your desired selection, group it via Select > Add > Group — this lets you re-select it later with one click. Useful when you find yourself repeatedly tweaking the same parts of the system.
Visual Feedback and Custom Filtering
Selections in SAMSON are visually indicated in the viewport, allowing you to verify before applying edits or simulations. For even finer control, the Document View hierarchy and Inspector panel show underlying node types and attributes — you can filter or manually select specific entries by their properties.
Combining these options opens up a powerful and streamlined workflow when dealing with large molecular assemblies.
Summary
Efficient selection eliminates noise and boosts focus. Whether you want to realign chains, simulate small fragments, or apply custom rendering effects, SAMSON provides surgical precision through its selection tools — all without needing scripts or complicated filters.
To learn more about the interface and see selection tools in action, visit the full documentation page at https://documentation.samson-connect.net/users/latest/interface/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.