I am trying to build a supercell for a molecular crystal starting from a .cif file that is in the literature (the beta form here: https://scripts.iucr.org/cgi-bin/paper?OS0098). I have been unable to open .cif files in Avogadro2, as I have posted about already on this forum, so I have been using Avogadro 1.2.0.
When I build a supercell by going to Build >> Super Cell Builder, and then entering the repeats (say, 5, 6, 4), I export to an .xyz file. Unfortunately, I see two problems: 1. some of the molecules are missing atoms (for example, there are less hydrogens than there should be based on the number of molecules), and 2. I can’t export the data such that the atoms are grouped by each molecule. How can I get around this?
For #2, I believe I can just write a code to calculate and sort nearest neighbors – though when I move on to non-orthorhombic crystals, this will presumably be more complicated. But #1 seems like a big issue…
Thank you in advance.