One common challenge in molecular modeling is the accurate orientation of molecular fragments when building new structures. Whether you’re assembling molecules from functional groups or trying to connect pre-defined assets, misaligned fragments can lead to structural errors that require time-consuming corrections.
SAMSON, the integrative molecular design platform, simplifies this with flexible features for orienting molecule fragments during the building process. This blog post introduces how to control fragment orientation in SAMSON for faster and more accurate molecule construction.
Why Fragment Orientation Matters
When building complex molecules by assembling fragments like functional groups, aromatic rings, or larger molecular subunits, it’s not just the bond that matters. The spatial arrangement affects bond angles, steric interactions, and ultimately the validity of your model.
Interactive Placement Options
SAMSON includes an Add editor that predicts fragment orientations and shows visual feedback:
- Green overlay: Acceptable substitution or bonding site
- Red overlay: Implausible or collision-causing placement
When connecting two molecular parts, SAMSON automatically attempts to position them to avoid atom overlap. This prediction works well, but what if you need even more control?
Manual Control with Move Editors
To fine-tune the orientation of a fragment after you’ve placed it, you can use the Local Move Editor or Global Move Editor (M and K shortcuts). This gives direct access to rotation and translation tools, including:
- Trackball rotation: Click and drag on the spherical interface to rotate.
- Axis handles: Rotate precisely around the X, Y, or Z axes.
- Pivot selection: Set a specific atom as the pivot to rotate your fragment around a bond or an anchor point.
Here’s an example of a user adjusting a fragment to fit a glycosylated scaffold:
Rotating Around Bonds
Sometimes, you just want to rotate around a specific bond to explore conformations. With the Local Move Editor, clicking on a bond automatically selects the connected sub-fragment and allows a direct rotation. This is useful for adjusting dihedral angles or exploring alternate binding configurations.
Here’s an example video from the SAMSON documentation that shows this in action:
Extra Tips
- You can use Ctrl / Cmd + click to specify which atom in a fragment should be used for substitution.
- The “Automatically orient fragments on substitution” option in Preferences > Editors > Add can be enabled or disabled depending on your workflow needs.
- If needed, use Shift + right-click to manually rotate the fragment before placement.
Conclusion
By combining predictive positioning, manual movement tools, and customizable preferences, SAMSON gives you full control over fragment orientation—solving a common source of modeling frustration. To explore these features further and improve your molecular assembly workflows, visit the full guide here:
https://documentation.samson-connect.net/users/latest/building-molecules/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.