v2.3.14.525

CueMol 2.3.14 (build 525)

This release is mostly about the 3D view. What the pointer is over is now decided
by the geometry the renderer actually drew, so a cartoon or a tube is hit anywhere
on the band instead of only near the CA; what is under the pointer is named in a
chip at the corner of the view and highlighted in place, without re-rendering the
scene. On the rendering side, overlapping translucent sections no longer invert
the ink they cover, a render no longer slows down when its window is covered, the
Rendering window's viewer keeps your framing across renders, and the GI lighting
ladder is rebalanced so a step changes only the fill. Several Coloring and
selection-list problems reported from use are fixed, including a click that used
to drop a list row into text-edit mode.

CueMol2 (the UXP app) is unchanged apart from the shared core, and keeps the
previous CPU hit test. CueMol3 is still a work in progress.

---

The 3D view: picking and hover feedback

Picking follows the drawn geometry. Hit testing used to work from the atom
positions, so cartoon, ribbon and tube renderers only responded within about 10
pixels of the CA -- the middle of a wide ribbon was dead. The view now picks from
an ID buffer drawn by the same geometry you see, so anywhere on the band hits the
residue it belongs to. Cartoon, tube, ribbon, spline, nucleic, trace, CPK, ANISOU,
ball-and-stick and simple renderers are covered.

The view says what is under the pointer. A chip at the bottom left of the mol
view names the element the pointer is on: chain and residue (plus the atom name
for atom-level renderers) on the first line, object and renderer -- and the
symmetry operation, if any -- on the second.

And it shows you where it is. The same element is highlighted as a translucent
fill with an edge band: a residue's worth of ribbon for cartoon-type renderers, one
atom for atom renderers. The highlight costs no scene redraw -- progressive
sampling is not restarted and ambient occlusion and anti-aliasing keep the quality
they had reached, so moving the pointer over a heavy scene does not send the image
back to its first pass.

Fogged-out geometry is no longer pickable. The pick pass reached one slab
depth further than the fog does, so hovering over what looked like empty space
produced a chip and a highlight. Both now stop where the picture does. Tube and
ribbon residue boundaries in the highlight are rings rather than a sawtooth.

The highlight survives the context menu. Right-clicking used to clear the
highlight the instant before the menu appeared. The hover is now held across the
menu and resampled when it closes, so after an action that moved the view
(Center at) the highlight is on whatever the pointer is now over.

Settings > Mouse & Navigation gains GPU Picking, Hover Info and
Hover Highlight switches. They take effect immediately and are remembered.

Rendering

Transparency: dark features no longer turn bright. In a scene with two
translucent sections, the pixels where they overlap were composited with a
negative background weight, which inverts contrast -- black edge lines over a
transparent surface came out white. A new per-pixel transparency mode weights
each pixel by the translucent layers that actually cover it, so the background
weight can never go negative and a lone layer keeps its exact alpha. It is in the
Rendering window under Transparency and is on by default; the previous layer
blend stays selectable as the reference for blendpng and POV-Ray parity. Rendering
time is unchanged.

A render no longer slows down when you look away. Covering or minimising the
window let Chromium drop the renderer process to an idle priority, which made an
umbreon render several times slower -- and it did not always recover, so the app
stayed slow until restarted. The renderer is no longer backgrounded, and while a
render job is running the system is kept from going to sleep.

The Rendering window keeps your framing. Zoom and scroll position are now
carried across re-renders and across Back / Forward in the history, so two
attempts can be compared at the same magnification instead of being re-zoomed each
time. If the image size changed, the zoom is corrected and the view re-centred on
the same part of the picture; the view fits only for the first image and when you
press Fit. The toolbar's + / - / 100% / Fit now hold the centre of the
viewport, pinch and Cmd+wheel still hold the point under the pointer -- and no
longer jump to the bottom of the image on every zoom.

The GI lighting ladder is rebalanced. A step now moves energy only from the
flat headlight into the ambient that carries the occlusion: the key light and the
average brightness stay put at every step, where the previous ladder also grew the
key light and so deepened the directional shading as you climbed. Step 4 remains
the default. Switching the lighting method to GI also enters at that default step
-- passing through a direct method (raytrace / AO) used to drop GI back to step 0,
because the direct methods' defaults coincide with step 0's values.

CueMol3: working in the app

Solid coloring reaches the molecule. Setting a surface to Solid coloring and
picking $molcol painted a half-transparent gray, and on dsurface / dsurf2
picking Solid coloring left the renderer on CPK coloring. Both are fixed, for
molsurf, isosurf and the direct-surface pair alike. One consequence: choosing
$molcol as the solid colour also leaves the flat colour mode, which is still
reachable through Reset to default style and, for isosurf, the Density map panel.

A click on a list row selects it; editing takes a deliberate gesture. The
scene tree entered rename mode on a click-pause-click, and a click anywhere in a
paint row landed in a text field -- so Cmd+C / Cmd+V / Cmd+Z went somewhere the
user could not see. A plain click now selects, and editing is entered on purpose:
double-click, Enter, F2, the context menu, or a visible affordance, and left with
Enter or Escape. The scene tree gains a Rename item in its context menu, which
it never had.

Copying and pasting paint rows works on the selection. Right-clicking a paint
row used to change the selection out from under the menu -- the same gesture acted
on one row or on all of them depending on where the focus already was -- and
Cmd+C / Cmd+V were taken by the text field under the pointer. Both are gone with
the rows no longer putting an input under the pointer.

The Named and History selection lists. all (*) now heads the Named list; it
is syntax rather than a stored definition, so selecting every atom previously meant
typing the expression from memory. The list's height now follows whatever hosts it
-- the Selection pane gives it the room the pane has left, and the popover takes
the room it actually has on the side it flipped to -- instead of a fixed five rows
for both. Embedded in a pane, the list is styled as a list rather than as a
dropdown left lying open.

Known incompatibilities and limitations

• GI lighting shows as Custom for scenes saved by an earlier build. The
  ladder's values changed, so a stored 1.2 / 0.05 / 0.4 matches no step. Pick a
  step again to take the new values.
• umbreon renders default to per-pixel transparency. A pixel covered by a
  single translucent section renders identically either way; pixels under two or
  more differ -- which is the fix. Switch Transparency back to the layer blend
  for blendpng / POV-Ray parity.
• The hover highlight is not drawn for symmetry-generated copies (those fall
  back to the CPU hit test, and picking them is unchanged), for renderers at alpha
  below 0.5, or in stereo. The overlay is drawn at half the backing resolution and
  is not antialiased.
• Rectangle and lasso selection still use the CPU hit test, so they keep the
  previous behaviour on cartoon-type renderers.
• GPU picking and the hover features can be turned off in Settings if a driver
  misbehaves; with GPU Picking off the view returns to the previous CPU hit test.

Downloads

• CueMol3 — CueMol3-2.3.14.525-macOS-arm64-Installer.dmg (macOS Apple silicon),
  CueMol3-2.3.14.525-Windows-x64-Setup.exe (Windows),
  CueMol3-2.3.14.525-Linux-x64.AppImage and CueMol3-2.3.14.525-Linux-x64.deb
• CueMol2 — cuemol2_2.3.14.525_macOS_ARM64.tar.bz2,
  ..._macOS_ARM64_py312.tar.bz2, ..._macOS_X64.tar.bz2,
  ..._Windows_X64.tar.bz2

These builds are not signed for distribution. See
tritium/packaging/README.md
for how to get past macOS quarantine and Windows SmartScreen.