chain breaks

I have been successfully using Mod4.0 to model multiple subunits together utilizing chain breaks in the alignment.

However this is causing problems in Mod6.0. I found in the manual for 6.0:

"For the time being, this and other alignment commands remove chain break information from the CALN array..." p.59

So this brings up several questions:

1) Is this the reason why I cannot create models with chain breaks in 6.0? 2) Is there an alternative solution besides sticking with Mod4.0 for the time being? 3) Is there an estimate on when chain breaks will be incorporated into Mod6.0?

Thanks in advance,

Christopher Wells MD/PhD Student Department of Pharmacology Medical University of South Carolina