Show molecular structures

[bast]

The reason why I did not do this yet is that the cube file does not "know" the structure. It only knows the positions. So we need some scheme to deduce bonds and/or additional formats.

[bskinn]

IIUC the usual simple bonding detection scheme is just to use interatomic distances, with bonds being rendered below a certain threshold distance.

Doesn't help for multiple bonds, though.

[bast]

Thanks! Do you know a reference table or a good starting point that I could use for this? Otherwise I can trial/error it. Maybe Bragg/Slater radii times some factor?

[bast]

Or are other codes using one general cutoff for any atom distance - irrespective of atom type?

[bskinn]

Hm. As of 2011, it looks like VMD only used a single cutoff for all atom pairs. Not sure what that cutoff was, though.

Ah! The second section here in the RasMol docs describes how they handle(d) it. Even includes a handy table of a few 2p distances.

[bast]

Super! Thank you! With this I can very soon add bonds.