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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

"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
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

Thanks in advance,

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