On Sep 12, 2018, at 6:48 AM, Matthias Bal <matthiascbal@gmail.com> wrote:

 And is there a way to script the conversion to treat files in batches?

Sorry, missed this part.  If you can get the naming issues ironed out, then this web page covers how to script through a set of data files:  https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html

—Eric

Eric Pettersen
UCSF Computer Graphics Lab