SAMSON Blog – Page 661

Controlling the Pace of Molecular Animations with Pause Frames

When creating molecular animations, one recurring challenge is controlling viewer focus. Things move fast—sometimes too fast. You might be trying to highlight a conformational change, emphasize a binding event, or pause at a molecular interaction that deserves more attention before…

Struggling With GROMACS Index Groups? Here’s a Simple Way to Manage Them Visually

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Creating and managing index groups in GROMACS can be tedious, especially when working with large biomolecular systems. Whether you’re setting up pulling groups, defining restraints, or preparing simulations, it often requires command-line scripts or careful hand-editing of selections. Fortunately, there’s…

Choosing What to Import After Your NVT Equilibration

OneAngstrom

After running molecular dynamics simulations, especially in tools like the GROMACS Wizard in SAMSON, a common question arises: What exactly should I import from my simulation? This may seem like a simple decision, but it can impact your analysis workflow…

A Quick Way to Align Molecular Structures in SAMSON

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Aligning molecular structures can be a repetitive task in molecular modeling, especially when working with multiple structures or preparing publications and interactive presentations. Minor misalignments can have a noticeable impact on how data is interpreted. But if you’re using SAMSON,…

Easily Select Residues Based on Charge and Polarity in SAMSON

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Working with complex biomolecular structures often requires isolating specific types of residues, such as those that are charged or hydrophobic. This task frequently arises in molecular modeling workflows—whether you’re designing mutations, analyzing ligand binding, or preparing systems for simulations. In…

A Simple Way to Validate Protein Structures Using Symmetry

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When modeling large biological assemblies like viral capsids or multimeric protein complexes, a frequent question is: does this structure actually make sense? Symmetry can be a powerful clue. Many biological assemblies exhibit some form of symmetry—cyclic (Cn), dihedral (Dn), or…

Reducing Docking Time with Smarter Search Domain Setup in Hex

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One of the most common challenges in protein-protein docking is the trade-off between accuracy and computational time. A full rotational search in docking can be very intensive, especially when you’re screening multiple systems or tweaking parameters. Fortunately, if you already…

A Simpler Way to Run AlphaFold-2 with SAMSON

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Predicting the 3D structure of proteins used to require extensive computational setups and technical expertise. For many molecular modelers, integrating AlphaFold-2 into their workflow means either accessing a command-line toolchain or relying on third-party web services — both of which…

From Click to Tube: Building Carbon Nanotubes with Your Mouse

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Creating realistic models of nanostructures like carbon nanotubes (CNTs) can be time-consuming and technically complex. For molecular modelers and materials scientists, the ability to rapidly generate customizable CNTs is often crucial for prototyping device components, performing simulations, or illustrating theoretical…

Fade Away: A Simple Technique to Transition Molecular Visibility

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Struggling with presenting complex molecular scenes in a clean, digestible way? If you often build animations to showcase conformational changes, protein-ligand interactions, or intricate visualizations involving multiple overlapping layers, you’ve probably asked yourself: How do I control what’s visible and…