only mark elements with an alpha above the picking threshold

src/mol-gl/shader/chunks/apply-marker-color.glsl

-float marker = vMarker * 255.0;
-if (marker > 0.1) {
-    if (mod(marker, 2.0) > 0.1) {
-        gl_FragColor.rgb = mix(uHighlightColor, gl_FragColor.rgb, 0.3);
-    } else {
-        gl_FragColor.rgb = mix(uSelectColor, gl_FragColor.rgb, 0.3);
+// only mark elements with an alpha above the picking threshold
+if (uAlpha >= uPickingAlphaThreshold) {
+    float marker = vMarker * 255.0;
+    if (marker > 0.1) {
+        if (mod(marker, 2.0) > 0.1) {
+            gl_FragColor.rgb = mix(uHighlightColor, gl_FragColor.rgb, 0.3);
+        } else {
+            gl_FragColor.rgb = mix(uSelectColor, gl_FragColor.rgb, 0.3);
+        }
     }
 }
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