3D Clean Up & Clean Up Structure

BRIEF DESCRIPTION:

After applying "3D Clean Up" to the molecule in ChemDraw and the following "Clean Up Structure" command the bonds are not corrected to the pre-defined "Fixed Bond Length" for current Style Sheet [Document Settings > Drawing], but simply interpreted as being projected to the monitor surface.

DISCUSSION:

Before introduction of "3D Clean Up" functionality, a purpose of "Clean Up Structure" command was to " to neaten the appearance of molecules by standardizing bond lengths and angles" [ChemDraw v21.0 User Guide, p.111]. Distorted bonds are getting rectified. Naturally, it is expected, that "3D converted" structure is simply returned back to 2D after "Clean Up Structure" command applied. However, during this step bonds are not normalized to the pre-defined fixed length. They are treated as projection to the screen view surface without length correction.

1. Using Benzene tool, draw 2 benzene rings.

2. Select second structure and apply "3D Clean Up" command.

3. Using "Structure Perspective" tool from the Main Toolbar, rotate it around X-axis approximately 45 degrees. Visually it appears fine.

4. Apply "Clean Up Structure" command. Observe, that obtained benzene ring is smaller - not identical to the first unmodified benzene ring. Bonds length doesn't reflect "Fixed Bond Length" setting for the document.

5. Repeating steps 3-4 give even smaller benzene ring structure.

The same behaviour is observed for any structure, that after "3D Clean Up" command has bonds non-planar to the screen surface. After "Clean Up Structure" command those bonds length is obtained as a simple projection to the screen view surface, the length of the shortest bond is chosen as a standardizing bond length for a whole structure without consideration of the Fixed Bond length setting of the current document.

EXPECTED BEHAVIOR:

After "Clean Up Structure" command for the "3D converted" structure bond lengths should be standardized according to the existing "Fixed Bond Length" settings of the current document.

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FILES:

3D Clean Up & Clean Up Structure.mp4

Windows 10 Pro, version 21H2, 64-bit OS Build 19044.1387,
Yoga 2 Pro (i7-4500U, 8GB), 13.3" high resolution QHD+ screen (3,200×1,800)
Intel HD graphics family (driver version 20.19.15.4642, driver date: 28/03/2017)
Windows OS Display settings for "Scale and layout" are: 250% (Recommended)
ChemDraw Beta v21.0.999.2240