Q:

I’m analyzing protein structures (specifically, I’m performing a Voronoi-based analysis) using the tools linked on the geometry page:

http://geometry.molmovdb.org/NucProt/

I’m using this on huge systems with more than 99,999 atoms. Is this possible?

A:
I don’t think there’s any hard coded limitation in the number of atoms. Look at the read_pdb_file routine this source script:

http://geometry.molmovdb.org/files/libproteingeometry/src-lib/readpdb.c

This "mallocs" up space on demand so in theory if you have enough memory I think you can accommodate >100K atoms. However, the PDB format itself is an issue here. You can modify the PDB reading routines to a different format. Just modify the read_record routine in the same file. However, I don’t know if doing this in multiple "models" will work.