HEllo Christopher,
Yes, it looks true.
In the older version (pre-release of mod6 and older) chainbreaks are OK in the alignment, in the current version (mod6v0) they cause problems. Only those chainbreak characters, that are within a sequence, not the ones, that separate heteroatoms.
On the other hand, you do not need to include them in the sequence, Modeller will automatically assume a chain break, if there is a longer than usual bond distance.
I hope, removing chain breaks from your seq will make your top file work, if not, let us know.
best wishes,
Andras
"Christopher A. Wells" wrote: > > 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