On 3/26/12 1:30 AM, vishal Nemaysh wrote: > Regarding this (3D structure prediction) problem sir i will try to find > out some template for covering the whole query sequence during BLAST. > but there is no any single template or multiple template are found to > occupied this query. so sir plz suggest me some solution...

Modeller is a package for comparative modeling, so if you have no template, you are out of luck. You either need to try harder to find a template (BLAST is not that sensitive - you can try other methods that use profile or HMM information, for example) or settle for only modeling the part of the sequence for which a template is available.

Ben Webb, Modeller Caretaker