Surface definition
Solvent-excluded surface (SES)
Construct the molecular boundary traced by a spherical solvent probe.
Generate a solvent-excluded molecular surface mesh
Build a triangular solvent-excluded surface from atom centers and radii, then inspect mesh geometry and topology.
Prepare
XYZR molecular coordinates
Use one to four XYZR files containing x, y, z, and atomic radius values in angstroms.
- Four finite whitespace-separated values per non-empty line: x y z radius
- Up to 5,000 atoms and 1 MiB in each XYZR Artifact
- At most 100 Å of coordinate span on each axis and 50 million estimated grid points
XYZR row
0.000 0.000 0.000 1.500Artifact media type
chemical/x-xyzr or text/plainHow the analysis starts
Choose a Project, open a compatible Dataset, then select the rows you want to analyze. Ubi will open this method with the compatible controls and column mappings ready to review.
Configure the scientific method
These controls appear in the Dataset analysis panel, where values can be checked against the actual input before the run starts.
Probe radius
0.5–3.0 Å; default 1.4 Å
Set the spherical solvent probe used to construct the excluded surface.
Grid scale
Fixed at 2.0
Use a consistent mesh resolution across comparable surfaces.
Review results as scientific outputs
Results open with the figures, structures, sequences, and metrics needed to answer the scientific question. Downloadable files remain available for downstream analysis.
How to interpret the result
- The surface depends on the submitted atomic radii, probe radius, and fixed grid scale; compare meshes only when these definitions match.
- Mesh area and topology describe geometry, not binding affinity, electrostatics, hydrophobicity, or experimental solvent exposure.
- Review atom links and source preparation before attributing local surface features to specific residues.
1
Molecular surface mesh
Inspect ordered vertices, vertex normals, atom links, triangular faces, bounds, area, and topology counts.
2
Surface geometry
Review mesh bounds, area, normals, atom links, and face orientation.
3
Topology checks
Inspect connected components, boundary edges, and other mesh-quality counts.
Continue your analysis
Use a complementary method on the same Project data.
Method scope and limitations
- This analysis generates solvent-excluded surfaces only; other NanoShaper surface definitions are not included.
- Oversized coordinate spans, grids, meshes, and malformed topology are rejected.
- Mesh geometry does not by itself describe electrostatics, hydrophobicity, or binding affinity.
