SAMSON Blog – Page 155

Selecting Atoms with Expressions: A Faster Way to Focus on What Matters

When working with molecular systems, one of the most common and repetitive tasks is identifying and selecting atoms of interest. Whether it’s isolating a solvent, highlighting specific residues in a protein, or selecting atoms based on spatial boundaries, this task…

Making Lights Work for You: How to Control Light Visibility in SAMSON

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When building complex molecular scenes in SAMSON, managing visibility can quickly become a challenge. Especially as molecular models grow in complexity, understanding how elements like light sources are displayed—or hidden—can save time and prevent errors during presentations, publications, or simulations.…

A Faster Way to Select Atoms with Mathematical Logic

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When working with complex molecular systems, one common challenge molecular modelers face is selecting specific atoms according to criteria that go beyond basic clicking or visual inspection. Whether it’s isolating atoms with a certain charge, picking out surface atoms, or…

How to Keep Your Camera Locked on Moving Atoms During a Simulation

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Tracking specific atoms during a molecular dynamics simulation can be challenging. As atoms move, rotate, and interact, your view can quickly become disoriented, making it difficult to focus on the region of interest. This is especially problematic when visualizing complex…

Quickly Select Residues with Specific Secondary Structure Using NSL

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When analyzing protein structures, molecular modelers frequently need to isolate specific regions like alpha helices or beta sheets. These are not just structural features — they often play specialized biological roles, from enzyme active sites to membrane-spanning domains. However, in…

Progressively Hiding Atoms to Highlight Molecular Mechanisms

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Creating compelling molecular animations is often an overlooked challenge for researchers and educators who aim to explain complex processes like ligand binding, protein folding, or chemical reactions. One common pain point is the need to visually remove unnecessary elements from…

Making Sense of Side Chains in NSL: What You Can Do with Side Chain Attributes

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When working with complex molecular systems, it’s easy to lose track of specific structural elements. One group that often requires more detailed attention is the side chains. Whether you’re filtering out noise, performing structure-based modeling, or setting up simulations, being…

Managing Visibility and Selection of Notes in SAMSON

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Anyone who works regularly with molecular modeling in SAMSON will tell you: clarity and control over your models can make a big difference. As your models grow more intricate—with annotations, labels, and multiple structural elements—being able to quickly show or…

Avoiding Common Pitfalls in Molecular Simulations with Constrained Animations

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One of the most frustrating issues for molecular modelers is running a simulation only to realize afterward that the initial positions of atoms weren’t quite right. The result? Drifting atoms, broken structures, or failed mechanical behavior. If you’ve ever tried…

Clarify your scenes: Filtering presentation nodes by visibility in SAMSON

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Working with complex molecular models often means dealing with countless nodes representing atoms, residues, structures, and their various visual representations. When presentation gets overwhelming, focusing only on visible content can dramatically enhance your workflow. That’s where SAMSON’s Node Specification Language…