Filtering 2D

[Josueok01]

Hello, I’m having troubles converting a set of molecules from 3D to 2D, just before this happens my dataset has nearly 8k compounds, the 2D Coordinates node filtered 1k compounds and I don’t know why, the structures are just fine, any ideas on what is happening?

Josué

[thor_landstrom]

Hey @Josueok01,

Welcome to the community!

Are you able to post your workflow here? It is hard to say why the filtering may be occurring. It could be related to conversion and the 2D node cannot properly port over all of the molecules which is why that may be occurring.

You may need to regenerate them to 2D based on your data, here is a thread that is related to rendering molecules to 2D from 3D:

Render molecule in 2D

Hi, I'm retrieving some data from a server in Mol2 format and converting it into a table of molecules.  We want to output this as a report, including molecular diagrams.  I'm using a "Renderer to Image" node to create the diagrams with the "Marvin" renderer.  However, this is producing 3D diagrams - which are not very useful as rings are sometimes tilted so that you can only see the edge.   Is there a way to tell the renderer to produce a 2D diagram by default? I've looked at the preferences b…

Hope this helps,
TL