ChimeraXWeb

ChimeraXWeb is the ChemistryAtlas web interface for UCSF ChimeraX-backed structural biology analysis and figure rendering. It combines browser preview with backend ChimeraX workflows for RMSD, contacts, H-bonds, clashes, surfaces, pockets, density fitting, and command-script execution.

Best For

• Structure superposition and RMSD analysis.
• Protein-ligand contacts, hydrogen bonds, steric clashes, and interface inspection.
• Surface area, pocket, and molecular-surface visualization.
• Density-map fitting and map/structure inspection.
• Publication-style figure rendering with ChimeraX commands.
• Reproducible ChimeraX command scripts from a web form.

Inputs

• Structure files: .pdb, .ent, .cif, .mcif, .mmcif, .mol2, and other ChimeraX-readable files.
• Ligand or density-map files when the selected workflow uses them.
• PDB IDs or pasted command/script text.
• Workflow choice such as superposition/RMSD, contacts, H-bonds, clashes, surface/pocket inspection, density fitting, publication figure, or command runner.
• Resolution settings such as 1200x900, 1800x1400, or larger publication sizes.

Upload And Preview Layout

The structure, ligand, or density-map upload controls sit above the preview window. Upload files first, confirm the preview structure is recognizable, then submit the backend ChimeraX job.

• The browser preview is for inspection and file confidence.
• The backend job is where ChimeraX analysis and rendering happen.
• Multi-file upload can be used for paired structure/ligand/map workflows.

Workflows

Structure Superposition / RMSD

Aligns two structures or chains and reports RMSD using the configured selection.

Protein-Ligand Contacts

Reports close contacts between receptor and ligand selections, useful for interaction review.

H-Bonds / Clashes

Runs hydrogen-bond or clash-style analysis to flag likely favorable interactions and steric problems.

Surface Area / Pockets

Generates surface-oriented inspection output for binding pockets, interfaces, and exposed regions.

Density Map Fitting

Loads map files and structure files for map/structure fitting workflows when ChimeraX supports the supplied formats.

Publication Figure Rendering

Runs style, color, camera, and resolution commands to produce a figure artifact.

Command-Script Runner

Runs user-supplied ChimeraX commands for advanced reproducible workflows.

Backend Requirement

ChimeraXWeb requires a UCSF ChimeraX executable in the backend container or sidecar. Set:

CHEMISTRYATLAS_CHIMERAX_BIN=/path/to/chimerax

or make chimerax available on PATH.

Docker installation also requires accepting the UCSF ChimeraX license before setting:

CHIMERAX_LICENSE_ACCEPT=1

If ChimeraX is missing or exits with an error, the job returns a clear failure and references chimeraxweb-run.log.

Troubleshooting

• If the browser preview works but the job fails, inspect chimeraxweb-run.log in the job output.
• If the backend reports missing ChimeraX, verify the binary path inside the backend container, not only on the host.
• If a map-fitting workflow fails, confirm that both structure and map files were uploaded and that ChimeraX supports their formats.
• If the result image is blank, simplify the script, load a known PDB file, and add style/camera commands gradually.

Acknowledgements And Validation

• ChimeraXWeb uses UCSF ChimeraX when installed and licensed by the operator.
• ChemistryAtlas adds browser upload, preview, workflow selection, generated scripts, logs, and downloadable artifacts.
• Validate structural biology conclusions against source structures, validation reports, experimental maps, and expert review.