Easily Undo and Redo Operations in SAMSON

When working on complex molecular models, it’s not uncommon to make an action you wish you could take back. Perhaps you moved an atom group the wrong way or applied a transformation prematurely. These situations are especially common during exploratory…

How to Select Metal Atoms in SAMSON Using NSL

When working with complex molecular systems, molecular modelers often need to focus on specific types of atoms for visualization, simulation setup, or analysis. For example, you might be preparing a study on metalloproteins or need to isolate metal ions in…

A quick tutorial on using Cycles in SAMSON

Cycles is the famed Blender renderer used by countless animators and VFX artists. We integrated Cycles in SAMSON to make it extremely easy to produce fantastic-looking molecular images and animations. Here’s a short thread that explains the 5 simple steps:…

Preparing proteins

To quickly prepare a protein structure in SAMSON (remove alternate locations, ligands, water and monatomic ions, and add hydrogens), click on Home > Prepare, select the steps you would like to include, and click Ok.

Integrating simulators with ASE

To quickly integrate simulators (e.g., XTB, ABINIT, BigDFT, LAMMPS, etc.) and use them in Python within SAMSON, you can use the Atomic Simulation Environment (ASE) package. This allows you to perform interactive and scripted calculations, simulate chemical reactions, etc. More…

Clipping structures

To activate clipping in SAMSON, hold Ctrl + Shift and click where you would like the clipping plane to be (or in the void to stop clipping). You can then use Ctrl + Shift + Wheel to move the clipping…

Freezing atoms positions

To control atoms mobility during minimization or simulation, use the Freeze (shortcut F) and Unfreeze (shortcut U) commands. Frozen atoms have a dark blue overlay in the viewport.

Selecting using natural language

/nsl is an undocumented SAMSON AI command that lets you use natural language to build selection expressions. For example, type /nsl atoms within 5A of the ligands, and SAMSON AI will translate it to n.t a within 5A of n.c…

Importing OBJ and glTF files

To enrich your images and animations in SAMSON, you can import OBJ and glTF files. You can then place them where you want and hit F9 to render using Cycles. You can also adjust their materials using the Inspector. Link…