Re: [Avogadro-Discuss] UNL after using Fill Unit Cell

[Geoffrey H. <geo...@gm...>]

> After importing my structure and checking the unit cell dimensions, I set the space group (5 c 2y c 1 2 1 as determined using Maestro) then select “Fill Unit Cell”. Visually, everything looks good. But unfortunately, all means of identifying the atom and the corresponding residue is lost in the exported pdb and 

The problem is that the "fill unit cell" does not necessarily match bonds and bond orders from the molecule. Consequently, when saving to PDB, the code attempts to perceive residues and can't match any of them (e.g., C-O instead of C=O for all amino acids).

While in your case, it might be reasonable to copy bond orders, in the general case, this is impossible since bonds can go across unit cell boundaries.

I don't know if Pymol will do this, but that would be my current suggestion- it has much better feature support for biomolecules.

Hope that helps,
-Geoff