Sextant · macromolecular crystallography suite

From diffraction images to a refined structure, in your browser

Sextant is a set of crystallography programs that run entirely in Chrome or Edge, on your own GPU. Image processing, molecular replacement, model building and refinement — one page, no installation, no server, and your data never leaves your computer.

Open Sextant Pipeline Get the files (academic licence)
Runs locally · nothing uploaded
WebGPU · Chrome / Edge 113+
Academic licence · free

Licence

AcademicFree for academic and non-profit research. Create an account with an institutional e-mail and accept the Sextant Academic Licence; after confirming the e-mail, the downloads are in your account. You may modify the programs for your own use; modified copies identify themselves as User Modified version.
IndustrialCompanies, CROs and paid services need a commercial licence. Write to licences@echolifesciences.com — we answer within two business days.
CitationCite Sextant (Echo Life Sciences) and the version printed in the program's output, e.g. Sextant Refine 0.2.32.0.

01 · Start here

Sextant Pipeline

The four core programs on one page, each in its own tab, with the output of one step feeding the next. Press Run pipeline and Sextant takes the decisions it can take on its own; the ones it cannot, it hands to you.

Sextant Pipeline 0.1.13

Drop diffraction images (or an MTZ, if the data are already processed), give the sample a name and a search model or sequence, and let it run. Every step saves its files with the sample name as prefix, or straight into a folder you choose.

  • Automatic pipeline with a decision flowchart coloured by confidence — a yellow or red step opens the decision for you
  • Space group, twinning and translational NCS tests before molecular replacement
  • Build is skipped automatically when the model already matches the sequence
  • Each program's version shown in its tab and written into every output file
  • Pipeline run file (JSON) that reproduces the whole run
Open Sextant Pipeline
01
Process
Index, integrate, scale and merge the images; choose the space group.
automatic
02
Checks
Resolution cut, anisotropy, twinning, tNCS, solvent content and copies per ASU.
asks when ambiguous
03
MR
Rotation and exact GPU translation search; packing and R-free checks of the solution.
automatic
04
Build
Trace chains and dock the sequence when the model is distant from the target.
skipped if sequence identical
05
Refine
Maximum-likelihood refinement, waters, TLS, NCS; validation and Table 1.
automatic
06
Refinement mode
Inspect density, fix residues, place ligands, make figures — then deposit.
you

02 · Core modules

The four programs, also on their own

Each module is a single page you can use independently — for example only Refine, on an MTZ from another pipeline.

Module 010.1.19.2

Sextant Process

Diffraction image processing on the GPU: Eiger HDF5/NeXus and Pilatus CBF (also inside .tar, .bz2, .zip), spot finding, indexing, profile integration, scaling and merging, space-group determination, anomalous output. A low-memory CPU mode for large datasets.

HDF5 · CBFMTZ outTable 1
Open Process

Module 020.1.10.2

Sextant MR

Molecular replacement with an exact translation search on the GPU (no FFT approximation), multi-copy search, packing analysis, translational-NCS and twinning tests, and refinement of the solution. Accepts PDB, mmCIF and AlphaFold models.

Exact GPU translation searchtNCS · twinning
Open MR

Module 030.3.3.8

Sextant Build

Automatic chain tracing into experimental or MR maps, sequence docking, loop closure and iterative rebuilding with refinement in between — for models far from the target or for experimentally phased maps.

Chain tracingSequence docking
Open Build

Module 040.2.32.0

Sextant Refine

Maximum-likelihood refinement with TLS, NCS restraints, twinning, anisotropic B, automatic waters and ligand dictionaries (eLBOW, AceDRG, Grade, CCP4). A refinement-mode editor with density, rotamers, mutations (including modified residues), ligand placement and publication figures.

ML refinementEditor · figuresmmCIF for deposition
Open Refine

03 · Derived tools

Built on the same engines

Specialised programs that reuse Sextant's processing, MR and refinement cores for the work crystallographers do at scale.

Derived 01

Sextant Events

Weak-binder detection across a fragment-screening campaign: ground-state model from the ensemble of datasets, Z-maps and event maps on the GPU (PanDDA-style), ranked events with density views, and export of the event models for refinement.

Fragment screeningZ-maps · events
Open Events

Derived 02

Sextant Batch

Hundreds of datasets through the same route — MR, refinement, ligand placement and a refinement-mode review per dataset — presented as a database: sortable statistics, flags for the ones that need a look, and a single export of models and tables.

Many datasetsDatabase view
Open Batch

Derived 03

Sextant Phasing

Experimental phasing (SAD) with autonomous decisions: substructure search, hand determination, density modification and a first model through Build — for targets without a search model.

SADSubstructure · hand
Open Phasing

Derived 04

Sextant Beamline Summary

The beamtime in one page: every crystal of every puck processed as it is collected — or loaded from the beamline's own autoPROC, XDS or DIALS results — with MR and refinement per crystal and a sortable summary of the whole collection. Load Example simulates a collection.

Live collectionPuck · crystal summary
Open Beamline Summary

All programs run in the browser and require a free Echo account (register · sign in); the academic licence is granted automatically to institutional e-mail addresses. Also available on request: Refine EM (real-space refinement for cryo-EM), Cloud (pharmacophore probability clouds from fragment ensembles), Active Site and MixedLigands.

04 · Sextant for Claude

The whole suite as an agent inside Claude

A bundle you add to your own Claude as a skill. Claude then opens the programs for you, reads their outputs, refines on the CPU in its sandbox, and modifies the programs for the analyses you need — with every result labelled by the version that produced it.

What Claude can do with it

  • Open any Sextant program as a page that runs on your GPU, and keep it updated as you work
  • Read logs, Table 1, refinement JSON and MTZ/PDB outputs; compare runs; plot statistics; write the methods paragraph
  • Run Sextant Refine on the CPU inside Claude's sandbox when you attach an MTZ and a model (no browser needed)
  • Change a program for you — a new output column, a different decision rule, a figure style — and publish it as your own version

Install

  1. Download sextant-for-claude-0.1.6.zip (academic licence; same registration as the files)
  2. In Claude: Settings → Capabilities → Skills → upload the ZIP. In Claude Code: unzip into ~/.claude/skills/sextant/
  3. Ask, in any chat: “open Sextant Refine”, “run the Sextant pipeline on these images”, “refine this model with Sextant on the CPU”, “make Sextant Process also write …”
Download Sextant for Claude Read the README

Requires a Claude plan with custom skills and Chrome or Edge with WebGPU for the browser programs. Claude is a product of Anthropic; Sextant for Claude is published by Echo Life Sciences and is not affiliated with Anthropic.

Versions are fixed — modifications are labelled

Every program in the bundle reports the version it was downloaded with, recorded with its SHA-256 in the bundle's manifest. When you or Claude edit a program, the copy is stamped as a User Modified version, and its page header, logs and every output file say so.

ProgramAs downloadedAfter your edits
Pipeline0.1.13User Modified version (base 0.1.13)
Process0.1.19.2User Modified version (base 0.1.19.2)
MR0.1.10.2User Modified version (base 0.1.10.2)
Build0.3.3.8User Modified version (base 0.3.3.8)
Refine0.2.32.0User Modified version (base 0.2.32.0)

So a methods section, a deposition or a colleague can always tell whether a result came from the distributed program or from a modified one. Echo supports the distributed versions; modified versions are yours.

Requirements

  • Chrome or Edge 113 or newer with WebGPU enabled (any recent NVIDIA, AMD, Apple or Intel GPU; 8 GB of GPU memory recommended for Process)
  • Nothing is installed and nothing is uploaded — files are read from your disk and results are saved back to it
  • Input formats: Eiger HDF5/NeXus, Pilatus CBF, MTZ, structure-factor mmCIF, PDB, mmCIF, restraint CIF (eLBOW, AceDRG, Grade, CCP4 monomer library)

How to cite

Until the paper is out, cite the software and the version printed in its output:

Sextant Pipeline (Sextant Process 0.1.19.2, Sextant MR 0.1.10.2, Sextant Build 0.3.3.8, Sextant Refine 0.2.32.0), Echo Life Sciences, https://www.echolifesciences.com/sextant/

Restraint library derived from GeoStd (BSD, Lawrence Berkeley National Laboratory). Questions, bugs and feature requests: sextant@echolifesciences.com.