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
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage