[modeller_usage] Builing models with big distances

[Fabio Passetti <fabio.passetti AT incor.usp.br>]

Dear all,

I am working on trying to build models of a protein that is shorter than 
the template. The gap between the model and the template is spatially 
big (~30 angstroms) and I could not configure modeller properly to deal 
with this. Up to now, modeller built models just deleting the part that 
I wanted, but it was unable to join the CAs of the remained boundaries 
of the deleted region. The models done by modeller always have two parts 
separated spatially: the before and the after the deletion. Does anybody 
have a guess how to solve this problem?

Best regards,

Fabio Passetti