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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?

example

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  • $\begingroup$ It's impossible to know without having the PDB file. Clearly there's a bug in handling the transforms (i.e., there's probably disorder), but we'd need the actual file. Please send it to the Avogadro list and I can comment further. $\endgroup$
    – Geoff Hutchison
    Commented Nov 9, 2016 at 15:34

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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.

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