On 08/04/2009 12:58 PM, Cool Hunk wrote: > 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 http://salilab.org/modeller/9v7/manual/node27.html

Ben Webb, Modeller Caretaker