Servalcat 0.4.142: Crystallographic Refinement Workbench

Input Structure & Reflection Data

Runs unmodified upstream servalcat refine_xtal_norefmac locally in a Web Worker. Drop your own coordinate (.cif, .pdb), reflection (.mtz), or ligand restraint (.cif) files anywhere on the page, or use the bundled RNase Sa benchmark.

Coordinates	rnase-bandicoot.cif 1SAR_BC · 1,474 atoms · 29 residue types (P2₁2₁2₁)
Reflections	rnasa-1.8-all_refmac1.mtz P 21 21 21 · 17,554 reflns · 16.32–1.85 Å · 13 columns
Ligand CIFs	Bundled CCP4 Monomer Library subset + on-demand fetch 0 custom ligand files staged (56 standard monomers bundled)

Amplitude (F)

Sigma (Q)

Free-R Flag (I)

Scattering form factor

Resolution limits (d_min – d_max Å)

Inspect all 13 MTZ header columns & datasets

Label	Type	Dataset	Min	Max	Assign

Refinement Parameterization

refine_xtal_norefmac

Cycles, Weighting & Hydrogens Core

Refinement cycles

Data-geometry weight Automatic weight adjustment

Starting weight:

Target bond RMSZ range

VDW repulsion weight

Hydrogen atoms

Output coordinates Write hydrogen atoms to output

Atomic B-Factors (ADP) & Coordinates ADP

Atomic B-factor model

B-factor restraint mode

B-factor restraint weight

Max ADP restraint distance (Å)

Reset initial B-factors (Å²)

Atomic positions Refine XYZ coordinates

Solvent, Jelly-Body, NCS & Link Restraints Restraints

Bulk solvent mask Include flat bulk-solvent contribution

Covalent & metal links Detect disulfide, metal & glycosidic links

Local NCS restraints Automatic local NCS restraints

Jelly-body restraints Enable jelly-body restraints

Jelly-body σ (Å) & d_max (Å)

d_max

Positional restraints Unrestrained refinement

Individual Geometry Term Multipliers Geometry

Passed via Servalcat’s REFMAC keyword parser into Geom.calc_kwds. Leave blank for upstream default (1.0); set 0 to disable a term.

Bond distances (dist)

Bond angles (angle)

Torsion angles (torsion)

Planarity (plane)

Chirality (chiral)

Pinned Wasm / Pyodide Supply Chain

36.0 MiB pinned

Every wheel and WebAssembly binary is verified against its SHA-256 Subresource Integrity pin in servalcat/manifest.json before execution. Unpinned network requests are rejected by the worker.

Artifact	Version	Size	SHA-256 Prefix
servalcat (wasm32 wheel)	0.4.142	526 KiB	fc8b2be8…
gemmi (wasm32 wheel)	0.7.5	1.34 MiB	a931d03c…
pyodide.asm.wasm	314.0.7	9.15 MiB	cc36e3ca…
scipy / numpy / pandas	1.18 / 2.4 / 3.0	20.19 MiB	c551e9af…

Table 1. Crystallographic Refinement & Model Statistics

Showing verified 5-cycle RNase Sa (1SAR_BC) benchmark baseline (native vs. Pyodide coordinate RMSD 1.0×10⁻⁶ Å). Click Run Servalcat to execute live in your browser worker.

Baseline reference · 5 cycles

Statistic / Parameter	Initial (Cycle 0)	Final (Cycle 5)	Shift (Δ)

Cycle-by-Cycle Convergence Trajectory

R_work (left axis) R_free (left axis) Bond r.m.s.Z (right axis)

Cycle 5 (Final) Rwork: 0.2492 · Rfree: 0.2901 · FOM: 0.7775 · Bond rmsd: 0.0095 Å (rmsZ 0.785)

Output Artifacts: Run Servalcat to generate downloadable out.mmcif, out.mtz (FWT/PHWT & DELFWT/PHDELWT), and out_stats.json.

Per-Cycle Refinement Ledger

Hover a row or plot point to inspect

Cycle	R_work	R_free	R_free − R_work	FOM	−LL	Weight	Bond r.m.s.d. (Å)	Bond r.m.s.Z	Angle r.m.s.d. (°)

Pyodide Module Worker Log Stream

Worker idle (loads on demand)

Ready. First execution fetches ~36 MiB Pyodide + Servalcat wheels (cached by browser afterwards).

Servalcat 0.4.142 (Python 3.14.2, Gemmi 0.7.5, NumPy 2.4.6, SciPy 1.18.0, pandas 3.0.2)
Target command: servalcat refine_xtal_norefmac
Benchmark verification against native macOS arm64 Servalcat 0.4.142:
  Atoms matched:     1474 / 1474
  Coordinate RMSD:   1.0e-06 Å (max shift 1.0e-05 Å)
  Rwork (cyc 0->5):  0.2535 -> 0.2509 -> 0.2498 -> 0.2493 -> 0.2492 -> 0.2492 (|ΔR| < 5e-07)
  Rfree (cyc 0->5):  0.2935 -> 0.2893 -> 0.2896 -> 0.2894 -> 0.2901 -> 0.2901 (|ΔR| < 5e-07)
  FWT/PHWT map rms:  3.3e-04 e/Å³ across 17,550 reflections

Click "Run Servalcat" above to execute live refinement in the Web Worker.