@matterhorn103 Passing the light into the dark scheme, the arrows of the gimbal and Cartesian coordinate system change from dark/black to bright/white. For consistency, I suggest this then equally applies to the tip of the pencil; else it appears as dull.
For comparison, based on the bright scheme copy pasted locally, I run the negation with ImageMagick by
Though it does not work particularly well for the icon about the template library, credit to this technique/snippet of code is due to Jimmy C. Kromann and his 2018-07-18 twitter tweet
I also took the opportunity to make the pencil a little darker yellow in light mode to improve contrast. This is similar to the measure tool being a different shade of the same colour in each mode.
I also made a flat version of the complex so that it fits in with the others.
I also thought about whether the function of the bondcentric manipulation tool might be clearer if the icon focussed purely on the idea of selecting a bond. I came up with:
The simpler symbols for (pen, complex, and now bond) improve the representation.
I do not see the first icon as too close to “measuring angles”, as there was very similar icon in the GUI of WebLab Viewer lite by Accelrys (a screen photo) as distributed in the late 1990s, or still in gabedit to indicate a 3D rotation of a selected structure.