[modeller_usage] Modelling a really large structure with a lot of chains

Dear Modellers,

I am trying to model a really large structure with a lot of chains (180 to be more exact - this is a complete virus capside) and I am encountering problems with the PDB format used in the automodel class. I manage to convince it to read a PDB file with 4 false chains (corresponding each to 45 "real" chains). However, the script finds out 180 chains internally (so much for fooling it...), writes them to the *.INI file with bogus chain IDs (and bogus residue and atom numbers) that it cannot read again when trying to produce the models. How to solve this? Can I change the automodel class to read mmCIF instead of PDB?

Thanks in advance,

Cláudio M. Soares