Patient Zero · VPatZero Primitive Protein Viewer

Input deck

Two PDB / mmCIF inputs

left molecule

1CRN.pdb

right molecule

3NIR.pdb

Drop one or two PDB, ENT, CIF, or mmCIF files here. The first fills left, the second fills right.

Starting viewer

Surface controls

Render and contact rules

Atom mode

Carbon load

Atom size

Bond opacity

Contact cutoff

Contacts are cross-molecule atom pairs inside the selected Å cutoff. Class labels are heuristics for inspection, not a docking score. Performance default: every other non-CA carbon is hidden on purpose.

Structure lens

Protein structure map

Color by

Backbone trace

Use this lens when you want the toy to teach. Primary, secondary, tertiary, quaternary, helix, and sheet are summarized at right. In secondary mode, the canvas colors helix, sheet, and loop directly.

Steering

3D scene controls

Drag action

Scene X

Scene Y

Scene Z

Blank-space drag orbits the scene. Protein rotation now lives in the compact A/B capsule. Drag X, Y, or Z directly to rotate on that axis, or click an axis and Shift-drag the protein. Ordinary drag still moves proteins. Right drag, Alt, or Ctrl shifts depth.

Docking

Rigid-body relax

One-button search. Molecule B samples small random rotations and shifts, keeps moves that lower the interface energy, sometimes accepts worse ones, then cools into a pocket on A. That is Metropolis simulated annealing: local rigid-body docking.

idlebest na

Heuristic scoring and local search, for exploration and teaching, not a validated affinity. The two built-ins are both crambin, so any pocket found is shape only. Load a cognate pair, for example barnase with barstar, for real interface biology.

Motion

Auto spin

Speed

Atom species filter

all shown

Tap a species row to toggle it. The filter affects both molecules and immediately rebuilds the contact ledger.

Live interface

Separated

contacts0 cutoff4.2 Å

minimumna visible0

Drag X, Y, or Z in a molecule capsule to rotate directly. Click an axis first for Shift-drag rotation.

full render · contact ledger live

ready

Contact ledger

Live counts

0left atoms

0right atoms

0contacts

naminimum Å

Separated0 visible atoms

Docking score

Interface energy

naa.u. · lower is better

No interfacebest na

shape

clash

elec

H bond

Sum of a smooth shape well, a bounded clash penalty, distance-dependent electrostatics, and an H-bond bonus over cross-molecule pairs within 6.5 Å. Drag the proteins together, or press Relax dock, and watch it fall.

Contact storm

Storm watch

pendingfirst strike

0/sstorm intensity

0 · 0front width A · B residues

0new flashes this pass

Draw cap0 of 1500

Clash warningclear

Storm mode flashes newly formed contacts. The live ledger may draw only the nearest contact subset when the interface gets crowded.

Structure guide

Six structure views

Primary

Sequence order pending.

Secondary

Local motifs pending.

Alpha helix

Helix ranges pending.

Beta sheet

Sheet ranges pending.

Tertiary

Whole-fold summary pending.

Quaternary

Assembly summary pending.

Canvas colors currently show atom species. Switch Color by to secondary structure to see helix, sheet, and loop directly.

Interaction classes

Contact mix

clash

H bond

ionic

hydrophob

near

Molecule ledger

Current structures

1CRN.pdb

visible0bonds0radius0 Å

3NIR.pdb

visible0bonds0radius0 Å

Elements

Atom species

Nearest pairs

Interactions

No contacts yet.

Scope note

What this is

Browser-native contact sandbox. It parses PDB and mmCIF atoms, centers structures, animates entry, lets users push molecules, and classifies close cross-molecule atom pairs by distance, element, and residue class. It is a visual triage tool, not a docking engine.

Patient Zero

VPatZero primitive build

architectureone HTML inputsPDB · mmCIF renderCanvas 2D networknone motion governoradaptive contact scanidle deferred

primitive intact