When we protonate some structures that depict certain carbon-carbon bonds as planar, they come back wedged either solid or slashed. I'm including an example from our database using tetracycline. Attached please find an example depiction of the structure for tetracycline, with an inset structure of the same compound after running the major microspecies code at pH 7.3. Notice that the position 5 carbon goes from being in the plane of the structure image to being below/behind the plane of the structure image.
We have a few other examples of this in our code. Is there a way to run a structure through the Marvin pKa calculator for the major microspecies at a given pH, and have it not modify these stereochemical bond orientation depictions? Is there some option to Marvin that I need to use in order to achieve this behavior?