When modeling molecules, minor tweaks can save significant time and help prevent structural errors. One of the most common frustrations for molecular modelers using design platforms is having to manually fix issues like overlapping atoms, inconsistent hydrogen counts, or unrealistic fragment positions after placing pieces together. If you’ve faced this, you’re not alone.
In SAMSON, a few builder preferences can dramatically improve your modeling workflow, making it smoother and more reliable from the moment you begin assembling atoms or fragments.
What Are Builder Preferences?
Builder preferences in SAMSON allow users to control how molecule components (atoms or fragments) are added and adjusted during the modeling process. These options influence things like hydrogen balancing, atom merging, and validation overlays that indicate allowed or disallowed substitutions.
Where to Find These Options
To check or modify these settings, go to Interface > Preferences > Editors > Add. Here you’ll find a list of checkboxes like:
- Adjust hydrogens when adding fragments
- Automatically orient fragments on substitution
- Merge neighboring atoms
- Prevent unexpected substitutions
- Select fragments after adding them
- Randomize orientations
- Create new structural models when adding non-covalent fragments
How These Settings Help
Here’s how enabling (or sometimes disabling) specific preferences can enhance your experience:
✅ Adjust Hydrogens Automatically
When adding fragments, SAMSON can automatically balance hydrogen atoms so you don’t need to manually edit every connection. This prevents valence violations and gets you closer to a chemically valid structure right away.
✅ Orient Fragments Smartly
By enabling automatic orientation on substitution, SAMSON intelligently rotates fragments to avoid spatial clashes, so your molecules look cleaner as they come together.
✅ Prevent Invalid Substitutions
Green overlays indicate valid binding points, while red ones help you avoid implausible chemical structures. This real-time guidance saves time and reduces the chance of building errors.
✅ Merge Overlapping Atoms
If you drag in a fragment close enough to another atom, SAMSON can merge them automatically—as long as chemical context allows it. This option can be toggled depending on whether you’re customizing or assembling standard components.
⚙️ When to Disable Features
If you’re working with non-covalently bound interactions (e.g. docking studies or supramolecular design), turning off Merge atoms and Adjust hydrogens may give you more control. Similarly, disabling orientation or hydrogen adjustments lets advanced users work out their own geometries.
Illustrated Example
Here’s what the preference panel for the Add editor looks like:
Conclusion
If you find yourself constantly adjusting hydrogen atoms or rotating fragments after placement, it might be time to look into SAMSON’s builder preferences. A few checked boxes can go a long way toward cleaner, more accurate models right from the start.
To explore these and more building features in detail, refer to the official SAMSON documentation: https://documentation.samson-connect.net/users/latest/building-molecules/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.