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:…
The fragmentation challenge Researchers in pharmaceutical companies are continually searching for better and faster ways to design drugs, but a long-standing challenge has been to juggle with independently designed software and data sources. Incompatible formats and workflows, disparate system requirements…
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.
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…
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…
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.
/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…
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…
To position molecules precisely, you can use translational and angular snapping. You can also choose any atom as rotation center.
To import and export molecules in a wide range of supported formats in SAMSON, use the importFromFile and exportToFile functions. Combine this with the getNodes function to quickly find atoms, residues, chains, binding sites, etc. and compute properties, edit molecules,…
