How to avoid the appearance of extra hydrogens from lattice packing of PDB file? I'm struggling with a pdb file of a unit cell that has a $\ce{CH3}$ which becomes a $\ce{CH6}$ when some software performs replication transformations. I've tried pack it with Avogadro and Mercury.

There is a way to avoid this by only changing something in the PDB file?
This is a bug, which is clear.

My guess is that you don't get $\ce{CH6}$ but that there's some disorder, so the transformations put two near-identical $\ce{CH3}$ groups on top of each other. Thus, one C becomes two, and each gains hydrogens.

There's usually a "slop" factor to detect near-equivalent atoms, but it's clearly failing.