Author: OneAngstrom

Streamlining Protein Management: Batch Preparation in SAMSON

Preparing proteins for docking, simulations, or other molecular design workflows can be time-consuming, especially when handling multiple structure files. SAMSON solves this challenge with its Batch Protein Prepare extension, making multi-file processing simple and efficient. Let’s explore how this tool…

Mastering Visual Model Attributes in SAMSON’s NSL

As a molecular modeler, have you ever found yourself struggling to efficiently fine-tune the visualization of specific elements in your molecular designs? The visualModel attribute space in SAMSON’s Node Specification Language (NSL) might just be the solution you’ve been looking…

Mastering the Undock Animation’s Movements in SAMSON

One common challenge molecular modelers face is achieving a clear and precise visualization when undocking molecules or parts of a structure. SAMSON, the integrative molecular design platform, provides a great solution with its Undock animation. However, many users might not…

Mastering Undo and Redo in Molecular Modeling.

Every molecular modeler has experienced this: You’re deep into designing a complex molecular system, carefully adjusting structures, and then… suddenly, a single unintended action derails your progress. Fear not—SAMSON’s History view has you covered! Let’s explore how leveraging the undo…

Ensuring Compatibility of SAMSON Extensions

For molecular modelers working with sophisticated software platforms like SAMSON, ensuring that all tools and extensions run smoothly can sometimes be a challenging task. This is where version compatibility becomes critical: each SAMSON Extension depends on specific versions of SAMSON’s…

Simplify Local GROMACS Setup with Custom Versions in SAMSON.

If you’ve ever worked with molecular dynamics simulations, you know that flexibility in software versions and configurations can be critical. Whether you’re aiming for reproducibility, need to use a specific GROMACS version, or want to fine-tune performance settings to suit…

Understanding the ‘numberOfAtoms’ Attribute in SAMSON

For molecular modelers, managing complex structural models often means navigating large datasets and sifting through intricate details about molecular structures. One common challenge is identifying specific models based on their atomic composition. Did you know that SAMSON’s Node Specification Language…

Effortlessly Track Center-of-Mass Motion in Molecular Systems

Molecular dynamics simulations reveal intricate details of molecular motion over time. However, understanding collective movements such as ligand unbinding or domain conformational changes can feel overwhelming when dealing with large datasets. Here’s an interesting solution for molecular modelers: SAMSON’s Pathlines…