On 03/31/2011 09:27 PM, Ashish Runthala wrote: > I am facing an interesting problem. Are gaps in target and template > same, as shown below. > > Target AAAAA AA--A AA--A > Template AA--A AAAAA AA--A > CaseI CaseII CaseIII > > Are these three cases I,II,& III modelled the same way. No. Case I is an insertion. The inserted region in the target (loop) will be modeled using just the CHARMM forcefield. Case II is a deletion - the template residues aligned with the deleted region won't be used. Case III is just a regular 1:1 alignment - since the gaps are in both target and template they are ignored. > How will the gap penalties be incorporated in these three cases, when > the modeller calculates the alignment score. Modeller does not use gap penalties in the modeling process, nor does it calculate an alignment score. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage