Actually i want to ask about a very common concept about modelling....
for this alignment, the red color representing beta strands is aligned
with gaps and its the template part wch is aligned wth gaps, my question
is how would this part be modelled??? would it be modelled a strand in
predicted model??? and what if any part of target is aligned wth gaps
but was conserdered a helix????? how would it be modelled..
Modeller extracts spatial restraints from the template(s), and combines
these with other physical and statistical data (e.g. CHARMM forcefield,
Ramchandran maps). So if there's a gap, you'll get a structure modeled
using only the physical and statistical data; Modeller doesn't do any
kind of secondary structure prediction. However, for such regions, if
you're reasonably confident of the secondary structure you can manually
impose a secondary structure restraint. An example is shown at