This ought to be pretty simple, but I'm not finding how to do it in MarvinSpace. I want my 3D aligned drug-sized molecules to show up in different colours for better distinction.
The help website clearly indicates that as a possibility (http://www.chemaxon.com/marvin/help/calculations/conformation.html) but I'm not able to reproduce in my situation, mainly because I haven't found the command to do so. Any help is appreciated!
You can also use alignment in MarvinSketch from the Calculations/Conformation/3D Alignment menu. You get the output poses with the colored molecules automatically, just as you expect.
This alignment can align two (or max 4-5) structures, that were previously added to the canvas of MarvinSketch.
Thanks for getting back to me. That's exactly what I've been doing, but I get the two molecules in the same color or color scheme. Is there any thing I should try? I have 4 molecules in the same .mrv file. I've tried erasing two of them of the MarvinSketch workspace before proceeding with the alignment, but I'm still unsuccessful in having them show in different colors.
I made two screenshots as an example for you. This shows that the 4 test molecules were coloured differently after alignment. Don't forget to check the Dislpay in MarvinSpace option to display the results in MSpace.
I hope this helps.