Re: [modeller_usage] Regarding protein 3D structure modeling

On 3/23/12 10:57 PM, vishal Nemaysh wrote: > i have an amino acid sequence and the length is (1106 amino acid). so > plz tell me how can i model the complete 3D structure of this much > lengthy sequence.

Modeller has no maximum length; modeling a large protein is exactly the same as modeling a small protein. You might have to tweak automodel.max_ca_ca_distance if the protein is especially large though: http://salilab.org/archives/modeller_usage/2011/msg00268.html

Ben Webb, Modeller Caretaker