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.
To create a Python app with a GUI, use PySide to add widgets and connect their signals (“clicked”, etc.) to slots (Python functions). Here is the complete code (65 lines) of a simple app with two buttons to add and…
To show molecules in the Goodsell Illustrative style in two steps, go to Visualization menu > Visual model > Visual Preset and choose Illustrative, then go to Visualization menu > Presets and choose Illustrative as well. The first step will…
