> and then the structure.pdb file is completely empty. The same thing happens 
> with Quantum Espresso files, although that's less unexpected since running 
> babel -H doesn't list Quantum Espresso as a suitable format (even though the 
> website claims the code can read these files). 

What version of Babel are you using?

babel -v
No output file or format spec!
Open Babel 2.3.0 -- Apr 21 2011 -- 12:24:58
Usage: babel [-i<input-type>] <name> [-o<output-type>] <name>
Try  -H option for more information.

If you don't see PWSCF, you're probably using an old version. But it's also 
possible that our support for these formats is incomplete. Since I'm trying to 
finish up the 2.3.1 release, I'd appreciate any test files for PWSCF or VASP 
that you could send me.

Thanks,
-Geoff
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