Ashika Umanga Umagiliya wrote: > I am new to Modeller and in the application I am developing , I have to > fully automate the modelling process.That mean,use only provide the > Sequence (in simple FASTA) format and I want Modeller to generate > structures for the sequence. > I saw that I can use 'automodel' class ,but I dont know the procedure > before using that class.

If that is your task, then you have a lot of work ahead of you. Building a model is the easy part - the hard part is selecting one or several templates, aligning your target sequence with the templates, and assessing the models after they are built. Modeller can do all of these steps (I suggest you work through the basic tutorial to see them) but they are not automated in Modeller itself. If you want automation, then Google for 'CASP' to see many examples, or use or own ModWeb server at salilab.org.

Ben Webb, Modeller Caretaker