Fix impostor clip zoom

examples/scripts/test/clip-dist-zoom.js

@@ -0,0 +1,72 @@
+// Regression scene for bonds vanishing on extreme zoom with clipDist = 0.
+//
+// Bonds (and ball+stick sticks) are drawn as cylinder impostors: a 4-triangle
+// bounding box that ray-casts the cylinder per pixel. Setting clipDist = 0
+// removes the floor on the perspective near-plane (viewer __updateClipping),
+// letting the camera get right up to a bond. Before the fix, the impostor box
+// corners were pinned to a clip-space depth near the far plane, so corners that
+// were still in front of the camera got clipped on zoom - half the bond would
+// disappear, then all of it. After the fix they stay visible until the camera
+// actually reaches the bond.
+//
+// How to test: run the scene, then scroll-zoom hard onto a single bond.
+// Press 'c' to toggle clipDist between 0 (zoom freely) and 10 (default floor).
+// Press 'o' to toggle perspective / orthographic and check both camera modes.
+// (In orthographic mode zooming magnifies rather than moving the camera in,
+// and gl_Position.w is always 1, so the near-clipping the fix addresses does
+// not arise there - the toggle is here to confirm no regression.)
+
+stage.loadFile('data://1crn.pdb').then(function (o) {
+  o.addRepresentation('licorice', { radius: 0.15 })
+  o.addRepresentation('ball+stick', { visible: false })
+  // Focus tightly on a few atoms so a bond fills the view straight away.
+  o.autoView('1-3')
+
+  stage.setParameters({ clipDist: 0 })
+})
+
+var textDiv = document.createElement('div')
+Object.assign(textDiv.style, {
+  position: 'absolute',
+  zIndex: 10,
+  top: '20px',
+  left: '20px',
+  color: 'grey',
+  fontFamily: 'monospace',
+  whiteSpace: 'pre',
+  pointerEvents: 'none'
+})
+stage.viewer.container.appendChild(textDiv)
+
+function _f (x) {
+  return (x || x === 0) ? x.toFixed(2) : '-'
+}
+
+function updateDiv () {
+  var sp = stage.getParameters()
+  var camera = stage.viewer.camera
+  textDiv.innerHTML = [
+    'Scroll to zoom hard onto a bond.',
+    "Press 'c' to toggle clipDist (0 <-> 10).",
+    "Press 'o' to toggle perspective / orthographic.",
+    '',
+    'camera:      ' + sp.cameraType,
+    'clipDist:    ' + _f(sp.clipDist),
+    'camera near: ' + _f(camera.near),
+    'cDist:       ' + _f(stage.viewer.cDist),
+    'bRadius:     ' + _f(stage.viewer.bRadius)
+  ].join('\n')
+}
+stage.viewer.signals.rendered.add(updateDiv)
+
+document.addEventListener('keydown', function (e) {
+  if (e.key === 'c') {
+    var next = stage.getParameters().clipDist === 0 ? 10 : 0
+    stage.setParameters({ clipDist: next })
+  } else if (e.key === 'o') {
+    var mode = stage.getParameters().cameraType === 'perspective'
+      ? 'orthographic'
+      : 'perspective'
+    stage.setParameters({ cameraType: mode })
+  }
+})

src/shader/CylinderImpostor.vert

@@ -124,8 +124,19 @@ void main(){
 
     gl_Position = projectionMatrix * w;
 
-    // avoid clipping (1.0 seems to induce flickering with some drivers)
-    // Is this required?
-    gl_Position.z = 0.99;
+    // Pin the impostor box to a fixed clip-space depth so its faces are never
+    // z-clipped; the true per-pixel depth is written later via gl_FragDepthEXT.
+    //
+    // The value matters: gl_Position.z is a raw clip coordinate while
+    // gl_Position.w still varies per box corner, and a vertex survives clipping
+    // only while -w <= z <= w. A value near the far plane (the old 0.99) forces
+    // w >= 0.99, so as the camera zooms in, box corners that are still well in
+    // front of it (small positive w) fail the far-plane test and get clipped -
+    // and because the box is only 4 triangles, losing a corner drops half, then
+    // all, of the cylinder. Pinning to 0.0 (the centre of the clip range) only
+    // requires w > 0, so corners are kept as long as they are in front of the
+    // camera. 0.0 is also the furthest from either clip boundary, avoiding the
+    // driver flickering that was seen at 1.0.
+    gl_Position.z = 0.0;
 
 }

src/shader/HyperballStickImpostor.vert

@@ -149,7 +149,14 @@ void main(){
 
     matrix_near = mat4( i_near, i_far, focus, e3 );
 
-    // avoid clipping
-    gl_Position.z = 1.0;
+    // Pin the impostor box to a fixed clip-space depth so its faces are never
+    // z-clipped; the true per-pixel depth is written later via gl_FragDepthEXT.
+    // gl_Position.z is a raw clip coordinate while gl_Position.w still varies
+    // per corner, and a vertex is kept only while -w <= z <= w. The old value
+    // of 1.0 forced w >= 1.0, so on extreme zoom box corners still in front of
+    // the camera (small positive w) were clipped, taking whole bonds with them.
+    // Pinning to 0.0 only requires w > 0, keeping every corner that is in front
+    // of the camera. See CylinderImpostor.vert for the full explanation.
+    gl_Position.z = 0.0;
 
 }