Separating part of mesh gives empty/invisible object

Question

I have a small molecule structure imported using the PDB/XYZ addon, and it imports all bonds of one type as a single object, In this case all carbon-carbon bonds. Id like to select the part of the mesh that makes up the highlighted C-C bond below and separate it to it's own object so I can apply a different material. I am in Edit mode, and have manually selected the vertices associated with the bond I'd like to separate.

However, after selecting these and pressing P then Separate by Selection, it creates a new object as if it worked, but the object appears to have no volume and is invisible/missing from all views other than as a line (shown below).

I have tried selecting a few things that do not work after doing this separation:

• New Edge/Face from Vertices - does nothing
• Reveal Hidden - does nothing
• Extrude Edges, Extrude Vertices, and Extrude Faces which all yield the same result, so it looks like maybe those dots have some volume to them? Not sure why it's doing this:

How can I recover this portion of the original object that was a cylindrical bond? I will have to do this many more times so hoping the fix is quick.

Answer 1

All the objects you can see in the 3D viewport are instances (linked duplicates) of other objects which are hidden from view. Therefore if you want to change an attribute of one of the visible objects you have to first select the corresponding instanced object and change it from there. The easiest way to do that is to select the hidden instanced part in the Outliner and change that objects material options.

In the example below we are going to change the Carbon bonds colour to green. The visible carbon bonds are made up of many instances of 2 hidden instanced objects. A short cylinder named Carbon_sticks_cylinder and capping faces named carbon_sticks_cup.

1. In the Outliner select the Carbon_sticks_cylinder.
2. Change the material colour to green. and we are done.

If you really need to have the bonds (and atoms) themselves editable then we have to make them independent of their "parent" objects :

1. Start by deleting the Carbon_sticks_cup object from the Outliner. We are not interested in the capping faces because they are inside the the bonds and would add a lot of unnecessary geometry (2 caps per little cylinder).

2.Select the relevant bonds then use Shft + H to temporarily hide everything else in the viewport.

3. Ctrl + A to open the Apply menu and choose the option Make Instances Real.

4. Next we join all the little parts to be a single object. Deselect everything A A then reselect all A and finally Ctrl + J. We now have the carbon bonds as a single editable mesh object.

5. We are left with a lot of overlapping vertices where the edge of each little cylinder meets its neighbour. To remove these, in Edit mode with everything selected use M to open the Merge menu and choose the By Distance option.

6. All that's left to do now is unhide all the parts we hid earlier. In Object mode Ctrl+H to Unhide.