rotation in 3D: mouse no longer tracks atoms

Please visit this page. Choose the first chair on the toolbar, and click on the canvas. Choose the Rotate in 3D tool, and rotate the structure vigorously. Now choose an atom such as N, and mouse over the different atoms of the chair as if you are going to replace a C with N. Note how the highlighting of the atoms doesn't track the position of the mouse. I think the internal coordinates of the atoms are not being changed when we rotate the structure. I would post a screen shot of what I mean, but my screen capture doesn't capture the mouse position. Using Marvin 14.9.8.0 on MacOS 10.9.5 with Safari 7.1.

Dear Bob,

Thank you for reporting this issue. The problem remains in the desktop version as well, and structure - independent, the 3D rotation mode causes this wrong behavior. I filed a report to our issue tracking system, and we will notify you if this issue has been fixed.

Regards,

Tamas Fazekas-Vigh

Any progress on this bug? It remains in the latest version of MarvinSketch.

BTW, workaround: after rotating the structure, highlight it, cut it, and paste it right back. That will reset the internal coordinates.

Hi Bob,

actually we are about to remove the rotation in 3D that is available via the F7 key, or an action that can be added to the UI by customization.

After we removed it, there still will be an option to rotate the structure in 3D (currently available by selecting the structure, and reach the 3D rotation tool by moving the mouse, or via Edit menu items), but not the view point, that creates a complete mess currently.

It seems to me that you use this functionality, so if we decide to remove this you will need a replacment to easily access the rotation function am I right?

Regards,
Istvan 

Absolutely, I use this functionality a lot.

I don't understand what you mean by, "there still will be an option to rotate the structure in 3D (currently available by selecting the structure, and reach the 3D rotation tool by moving the mouse, or via Edit menu items), but not the view point." Do you mean that in the future, the act of rotating the structure will change the xyz coordinates of the structure as well? If so, that's just fine. I don't mind that the xyz coordinates will change when I rotate the structure; in fact, I would expect it.

Hi Bob,

I mean exactly that the coordinates will change, that was our expression also that the users can not really distinguish between these two rotation types, and only the one that changes the coordinates are meaningful for them. So that is why we decided to remove the other functionality.

This is in our plans, I am not sure about the schedule yet though.

Regards,
Istvan

I notice that this bug has not been fixed as of Marvin 15.11.23. I place the chair cyclohexane conformer (Insert -> Template Library -> Conformers) in the MarvinSketch window, choose View -> Transform -> Rotate in 3D, and rotate the structure. Then I choose the Bond tool and hover over a bond to convert it to a double bond. Sometimes Marvin highlights the bond I hover over, sometimes it highlights a different bond, and sometimes it doesn't highlight any bond at all.

Yes, it looks like the root of problem is the same. Thank you for the additional info.

Best regards,

Efi