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…

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Create molecules using Python

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…

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Illustrative style in two steps

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…

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Rotating fragments around bonds

To rotate a molecular fragment around a bond, use the Local Move Editor (shortcut M) and just click on the bond. The editor will automatically select the shortest fragment and will show the move widgets. Combine this with interactive minimization…

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