Uncategorized – Page 868

Cleaning Hundreds of PDB Files Doesn’t Have to Be Painful

If you’ve ever tried to prepare dozens or even hundreds of protein structures for simulations or machine learning, you know how quickly things can become tedious. Downloading PDB files, stripping water and ions, resolving alternate locations, adding missing atoms… And…

Avoiding Selection Frustration: A Quick Guide to Node Group Attributes in SAMSON

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When working with complex molecular models, it’s common to group atoms, residues, or entire molecular structures for easier manipulation. But as models become larger, selecting and filtering node groups effectively becomes a challenge. If you’ve ever struggled to isolate just…

Avoid Simulation Headaches: Add Custom Index Groups During Equilibration or Simulation

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Preparing molecular simulations in GROMACS often involves defining specific atom groups — known as index groups — for tasks like pulling, restraints, or targeted measurements. GROMACS automatically generates standard groups (e.g., for protein, solvent, ions), which often suffice. But sometimes,…

Why Molecular Modelers Should Claim Their SAMSON Profile (And How to Make It Shine)

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When collaborating with teams or sharing your molecular modeling work with the broader community, how you present yourself online matters just as much as the quality of your research. For users of SAMSON, the integrative molecular design platform, a customizable…

Avoid Ligand Confusion: Correctly Selecting Ligand Atoms in Ligand Path Finder

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One of the most common setup issues encountered by molecular modelers working on protein-ligand interactions is an incorrect definition of the ligand itself. This can lead to inaccurate path predictions, unexpected energies, and even failure of the algorithm to find…

A Simple Way to Play Trajectories in Reverse with SAMSON

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When analyzing molecular structures and motions, it’s often helpful to step back—literally. While forward trajectories offer valuable insights, playing molecular paths in reverse can highlight subtle interactions, simplify comparisons, or illustrate transitions between conformations more clearly. This is especially useful…

Following Atoms with the Camera: A Simple Way to Frame Better Molecular Animations

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Creating molecular animations can be incredibly powerful when trying to convey structural mechanisms or simulation results — but getting the camera to follow atoms precisely in 3D space is often a challenge. Whether you’re highlighting a docking process or zooming…

How to filter molecular bonds by length in SAMSON’s Node Specification Language

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When working with molecular models, identifying bonds of specific lengths is often essential. Whether you’re analyzing structural changes, refining a force field, or creating visualizations that focus on specific bonding regimes, quickly filtering for bond lengths can save a lot…

Struggling with molecular file types? Here’s how SAMSON handles them.

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One of the most persistent issues that molecular modelers face is dealing with the variety of file formats present in computational chemistry and structural biology. Between .pdb, .mol2, electron density maps, and dozens more, managing the import process often becomes…

Duplicating Molecular Structures Without Scripts or Spreadsheets

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As molecular modeling projects grow in complexity, manually duplicating and arranging molecular structures can quickly become tedious. Whether you’re assembling a nanotube from scratch or building repeating motifs in materials science or biomolecular models, the goal is the same: replicate…