atom color in MarvinSpace 6.1.3

Hello,

I am posting with a question regarding the free version of MarvinSpace 6.1.3.

I was wondering if there is any way to selectively change the carbon atom color for 1 compound over another, so that when they are aligned one compound is easily distinguishable from the other?

Many thanks in advance,

Velvet 

Hi,

yes, it is possible to view the aligned structures exactly as you want, but not in MarvinSpace. Just open two structures in the same canvas in MarvinSketch and select Calculations/Conformation/3D Alignment, then simply press OK. The resulting alignment pose is visualized as attached, where the coloring is by CPK in the left view, and by the structures on the right.

The aligned coordinates can be transported back to MarvinSketch for further processing from the right-click context menu.

Kind regards,

Adrian