Open supported scientific files from Files or a result link. OpenScience selects a view based on the file and its contents. Use Source where available to inspect the original representation, and Download when you need a specialist application.
Structures and molecules
| Input | View and interpretation |
|---|---|
| PDB, ENT, CIF/mmCIF, PDBQT, GRO | A 3D structure view for supported structure data. |
| SDF, MOL, MOL2, XYZ | A 3D molecular view when valid coordinates are present. |
| SMI or SMILES | A 2D depiction of the first molecular record; the file can contain additional records. |
A valid display does not establish correct protonation, stereochemistry, biological assembly, or experimental quality. Ask for the source accession, chains, ligands, and any missing residues relevant to your question.
Open structures/target.pdb. Identify the chains and ligands, explain what
is represented, and list checks needed before using it for docking.
Preserve the original structure.
Sequences and alignments
FASTA-family files open as sequence views. Multiple records of the same length can open as a multiple-sequence alignment; unequal-length records may show the first sequence with a record count.
Equal lengths alone do not prove that sequences were meaningfully aligned. Ask which method produced the alignment, whether gaps were retained, and which sequence set it represents.
For a multi-record collection, use an analysis tool to inspect every record rather than assuming the first displayed sequence summarizes the collection.
Reads, variants, and annotations
| Format | Available inspection |
|---|---|
| FASTQ/FQ | Read lengths, sequence composition, quality summaries, invalid records, and sample records. |
| VCF | Variants, samples, reference metadata, chromosome/filter summaries, and displayed variant records. |
| BED | Intervals, chromosome summaries, spans, and feature rows. |
| GFF/GFF3, GTF | Annotation features, feature types, strands, and intervals. |
| SAM | Alignment summaries, mapping flags, reference information, and sample alignments. |
| mzML | Mass-spectrometry file summaries and supported spectrum metadata. |
Some previews analyze a bounded portion of the file. Inspect truncation notices and ask for full-file quality checks before drawing quantitative conclusions.
BAM, CRAM, and single-cell files
BAM and CRAM inspection depends on appropriate local tools and, where required, index/reference files. H5AD and Loom views can inspect dimensions and metadata; available stored embeddings can be shown when the inspection succeeds.
These formats are not ordinary text files. If a prerequisite is missing, follow the reported setup requirement or use a prepared summary generated by your analysis environment. Do not rename a binary file to CSV to make it readable.
Genome tracks
The workspace can render configured genome-track results with the genome, locus, and supported track resources supplied by the analysis. Opening an arbitrary BED or VCF file as a table is different from preparing a genome-browser view.
Specify the reference assembly, chromosome naming, coordinate convention, and track indexes. A mismatch can place a feature at the wrong location or prevent a track from loading.
Review and share a view
Ask for an explanation of colors, labels, coordinates, and selected records. If you need a figure for sharing, request a saved image and its caption, with the original scientific data preserved separately.
Use Genomics or Molecular research to turn inspection into an analysis. Use Figures for an exported scientific figure.