SAMSON Blog – Page 176

How to Add Custom Backgrounds to Molecular Presentations in SAMSON

When creating molecular presentations, visual clarity contributes significantly to the understanding and impact of your work. One common challenge molecular modelers face is: how can I make my presentation visually coherent while transitioning between multiple views? This is especially relevant…

How to Sketch New Molecules in 2D with SAMSON’s Interaction Designer

OneAngstrom

Designing molecules often starts with a good sketch. But many molecular modeling tools lack an intuitive way to draw molecules while simultaneously seeing their 3D structure evolve. If you’ve ever wished you could build and edit molecules directly in 2D…

Easily Undo and Redo Operations in SAMSON

OneAngstrom

When working on complex molecular models, it’s not uncommon to make an action you wish you could take back. Perhaps you moved an atom group the wrong way or applied a transformation prematurely. These situations are especially common during exploratory…

How to Select Metal Atoms in SAMSON Using NSL

OneAngstrom

When working with complex molecular systems, molecular modelers often need to focus on specific types of atoms for visualization, simulation setup, or analysis. For example, you might be preparing a study on metalloproteins or need to isolate metal ions in…

A quick tutorial on using Cycles in SAMSON

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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:…

Transforming Molecular Design: OneAngstrom Integrates NVIDIA BioNeMo into SAMSON

OneAngstrom

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…

Preparing proteins

OneAngstrom

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.

Integrating simulators with ASE

OneAngstrom

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…

Clipping structures

OneAngstrom

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…

Freezing atoms positions

OneAngstrom

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.