Complex geometries + packing + regions

Dr. Kohlmeyer, thanks for that (very) comprehensive reply.

I just want to make sure I’m on the same page as you: when you say VMD, you’re implying I should write a script in matlab or python that reads the raw .xyz file and processes it accordingly, right? The actual “VMD” program looks like an animation tool…

Thanks,
-h

Dr. Kohlmeyer, thanks for that (very) comprehensive reply.

I just want to make sure I'm on the same page as you: when you say VMD,
you're implying I should write a script in matlab or python that reads the
raw .xyz file and processes it accordingly, right? The actual "VMD" program
looks like an animation tool...

no, VMD has an embedded Tcl (and python) script interpreter
and adds several extremely powerful domain specific commands
to the script language that make scripting very powerful. a large
number of tools for system setup, analysis and visualization
- including topotools - have been written based on the VMD/Tcl
script interpreter. there are some peculiarities to it, since it was
originally conceived for handling bio simulations, but one get
quickly used to it.

of course, you are free to write your own tools in any language
you like. many people do this, too.

axel.