Respected sir, I B.Nataraj,recently (two days back) started using modeller under academic liecese . I am right now modelling a transmembrane protein for which I know the topology,and other important structural component such a pore selective filter region , transmemrane segment region etc.,, and template that I using is also having another transmembrane region of simillar topolgy and everything. but sequence similarity is 19% , since I know the secondary structural element of my target sequence I want to assign those part of my sequence to the template and proceed to modelling , my question is 1) whether my this idea is possible with help of modeller command or scripting. can you give me the script to stright way of doing this, since I feel bit uncomfortable to do modelling in command mode , as I used to be in graphical interface so for .

Thanking you,

B.Nataraj, II M.Tech.(Bioinformatics), SASTRA Deemed University, Thanjavur, Tamil Nadu, India.

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