# Drybench Cell: methods and checks

How Drybench Cell reaches its results: every calculator, analysis or view with its methods, the references behind them, how far each has been checked, and the app's limits.

[Open Drybench Cell](https://www.drybench.com/cell/app) · [What the levels mean](https://www.drybench.com/methods/levels) · [Every app's methods and checks](https://www.drybench.com/methods)

## The tour

Eight steps from DNA to a working protein, each a published structure trimmed to what the step shows, with its primary citation and its measured sizes.

No method record is kept for this step, so it carries no level.

### How it is made and tested

- The stored reference records: each PDB entry's title, method, resolution, dates and organisms from the RCSB Data API, each primary citation checked against Europe PMC, and each UniProt accession.
- Every PDB entry matches the RCSB record, every citation matches Europe PMC, the numbers in the copy are the measured ones, sizes and the colour key match the scene data, links use verified human UniProt accessions, and every step has a still within the size budget.
- The palette matches the pipeline, every scene builds a MolViewSpec tree, labels can be switched off, scenes carry no camera transition, and zoom stays within limits.
- Every shipped structure file is gzipped BinaryCIF and unzips; a stalled download fails with a timeout, a slow one is not cut off, and cancelling and server errors are reported.
- **Structures:** Eight PDB entries, trimmed to the atoms shown, with no water or hydrogens; gzipped BinaryCIF files of 25 to 240 KB.
- **Large complexes:** The spliceosome, TREX, the two ribosomes and TRiC keep one atom per residue for the machinery, and every atom for the RNAs and chains the step is about.
- **Stills:** Blender 5.2 with the Molecular Nodes add-on, Cycles on the CPU, 32 samples with denoising, from the same scene data as the 3D view.
- **Scale:** Sizes are in nanometres; 1 nm is a millionth of a millimetre. The eight structures come from separate experiments published between 2006 and 2025, so they show the stages of making a protein, not one molecule passing through them. All the proteins are human. The RNA being spliced in step 3 is listed as coming from an adenovirus, and in step 5 the message is synthetic and the tRNAs have a bacterial sequence.

## Data sources

- [RCSB Protein Data Bank](https://www.rcsb.org/pages/usage-policy): CC0 1.0
- [UniProt](https://www.uniprot.org/help/license): CC BY 4.0
- [Europe PMC](https://europepmc.org): EMBL-EBI terms of use (no added restrictions)
- [RNAcentral](https://rnacentral.org): CC0 1.0
- [PDB-101 Molecule of the Month](https://pdb101.rcsb.org/motm/motm-by-title): Articles © RCSB PDB and authors; background reading only, no text reused
- [Mol\* 5.11.0](https://molstar.org): MIT
- [Blender 5.2 (bpy 5.2.2)](https://www.blender.org/about/license/): GPL-3.0-or-later for Blender binaries such as bpy (source GPL-2.0-or-later); build-time tool only, no code shipped
- [Molecular Nodes](https://github.com/BradyAJohnston/MolecularNodes): GPL-3.0-or-later; build-time tool only, no code shipped
- [Biotite](https://www.biotite-python.org): BSD-3-Clause
- [NumPy and SciPy](https://scipy.org): BSD-3-Clause

## Limits

> This is an educational illustration, not a research or clinical resource.

- The steps are separate experiments on different molecules, from different laboratories and years. They illustrate the stages of gene expression; they are not one gene being followed through the cell. The scenes combine species and experimental systems, including synthetic components and trapped or drug-stabilised states.
- Structures are snapshots. Flexible parts, such as histone tails and most of the mRNA held by TREX, are missing from the models, and the machines move between many states that one structure cannot show.
- For the spliceosome, TREX, the two ribosomes and TRiC, the 3D view draws the machinery as a backbone trace (one point per residue) to stay light on phones. The key RNAs and chains keep every atom, and the full entries are one click away on the RCSB PDB.
- Some complexes were trapped with a drug or assembled from synthetic parts: step 5 has the drug cycloheximide, a synthetic poly(U) message and tRNAs with a bacterial sequence, and step 6 has the stalling molecule PF-06446846.
- Cutaways and camera angles were chosen to show the step's subject; they hide parts of each complex.
- This is an educational illustration, not a research or clinical resource.