Animating molecules
To animate atoms moving and deforming in SAMSON, select them and add a Move atoms animation to your presentation. You can then add and control multiple keyframes that SAMSON will smoothly interpolate for you.
Generating symmetric replicas
To quickly add symmetric replicas in SAMSON, use the Symmetry Mate Editor. This free extension lets you interactively generate symmetry mates of a protein based on the crystallographic information from a PDB file.
Making SAMSON AI ✨ do something
To make your SAMSON AI do something, begin your prompt with /do. And if you prefer to speak, just say do (turn the sound on for the video example below). This is an example of retrieval-augmented agency (RAA), where knowledge…
Creating an assembly animation
To quickly create an animation of two or more molecules assembling, select them and double-click the Assemble button in the Animator (Ctrl / Cmd + 7). This will automatically determine the initial and final position of each molecule, and add…
Editing side-chain conformations
To edit protein side-chain conformations in SAMSON, use the Rotamers editor extension based on Roland Dunbrack’s famed library. Select a residue, then choose the rotamer you want to use from the corresponding table. Potential clashes will be automatically detected and…
Creating replicas of structures
To create replicas of structures using SAMSON’s Python API, call their clone() function. You can then programatically edit these structures. The example below shows how to start from a single nanotube to create a model of a nanotube “fabric” through…
Making molecules refractive
To make molecules refractive when you use Cycles in SAMSON, increase the transmission coefficient. You can also directly use Appearance presets to quickly change multiple coefficients at the same time. Check the YouTube short at https://youtube.com/shorts/VAh9N03G8q4.
Quick geometry optimization using the FIRE minimizer
To perform very fast geometry optimization, use the FIRE minimizer. When this carbon nanotube is sliced, it quickly relaxes to a mostly flat graphene sheet.
Accessing the data graph in Python
To efficiently manipulate nodes (atoms, bonds, side chains, molecules, etc.), use node indexers returned by the SAMSON.getNodes function applied to a Node Specification Language (NSL) expression. For example, SAMSON.getNodes(‘node.type atom’) returns an indexer containing all atoms in the active document.…
Creating a nanopore
To build a carbon nanopore, draw a graphene sheet and a nanotube, remove some atoms and use the Brenner reactive force field during interactive minimization to meld them. The Brenner potential (Brenner et al., Journal of Physics: Condensed Matter, Volume…