SAMSON Blog

From sudden pop-in to gradual reveal: presenting molecular models with Appear

A molecular model can be scientifically clear and still be difficult to follow when it appears all at once. In a presentation, that sudden change may distract from the structure you want people to notice. A gradual reveal offers a…

From molecular path to usable coordinates: export only what your analysis needs

OneAngstrom

A molecular path can be easy to inspect on screen and surprisingly awkward to use in a downstream workflow. If you need a ligand’s changing coordinates for a reaction-coordinate analysis, for example, exporting every atom may leave you with far…

The handoff checklist: sharing molecular work without losing the thread

OneAngstrom

A molecular modeling task rarely ends at the moment one person saves a document. A collaborator may need to inspect a structure, continue an analysis, run a job, or simply understand what has already been done. When the work moves…

Find the Right Files Without Losing Track of Selection

OneAngstrom

When a molecular project contains many files, a small mistake in a filter can make it harder to find the structure or supporting file you need. SAMSON’s Node Specification Language (NSL) provides a way to describe file nodes using attributes…

Stop Rebuilding the View: Keep Useful Molecular Perspectives Ready

OneAngstrom

You have a molecular structure framed just right: the region of interest is centered, the scale feels useful, and the surrounding context is still visible. Then you zoom in to inspect a detail—and the original view is gone. Recreating it…

Find the Molecules You Need Without Counting by Hand

OneAngstrom

A crowded molecular model can make a simple task surprisingly slow: finding the molecules that are small enough to inspect, contain enough residues to be relevant, or have a particular chain structure. Counting atoms or residues one molecule at a…

A calmer workflow for building and editing molecular structures

OneAngstrom

Editing a molecular structure can become frustrating when every change seems to create another decision: should you move the structure, build onto it, repeat it, or relax its geometry? A useful way to reduce that uncertainty is to separate those…

Before the First Molecule: A Smoother SAMSON Install

OneAngstrom

A molecular modeling session can lose momentum before it begins: the installer cannot connect, the account key is nowhere to be found, or a proxy setting gets in the way. A little preparation can make the setup more predictable. This…

When Molecules Don’t Fit: A Practical Workflow for Building with Fragments

OneAngstrom

Building a molecule from fragments can save time, but it also creates a familiar problem: a fragment may land in an awkward orientation, overlap nearby atoms, or produce a connection that is chemically implausible. Adjusting the structure by trial and…

When a molecular workflow hits a wall, find the right extension

OneAngstrom

A molecular modeling workflow rarely breaks because of one dramatic problem. More often, it slows down at a familiar bottleneck: a file needs a parser, a repetitive task needs automation, a structure needs a specialized visualization, or a simulation needs…