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…
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…
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.
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.
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.…
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…
To create molecules, Python bindings give you access to all modeling capabilities from SAMSON’s C++ core. Add atoms, bonds, molecules, crystals, automatically find covalent bonds, add hydrogens, etc., and minimize. All in a few lines. Use the Code Editor to…
To trigger any GUI command in Python, call the SAMSON.runCommand function on the command name. Use this directly in the Python console (Ctrl / Cmd + 8), or in Python scripts to automate tasks using the Code Editor (Ctrl /…
To quickly change the look of objects when rendering with Cycles in SAMSON (Trace mode, shortcut F9), first apply a material, then apply an appearance preset in the Inspector.
To build molecules, use A to add atoms and fragments, B to edit bonds, and C to edit charges. Combine this with interactive minimization (shortcut Z) to build physically-based structures.
