On 6/24/10 9:58 AM, Piyush Diyora wrote: > My question is > 1) As these fragments are from different protein having different 3d > structure, HOW RELIABLE WILL BE MY PROTEIN 3D STRUCTURE?
You can't tell for sure. Input alignment and sequence identity are poor indicators of output model quality. This is the job of model assessment. But when you have multiple templates, you should be particularly careful in the regions where they overlap, since they may give contradictory information.
> 2) If I want to build a model based on the reference template (created > by joining all the fragments), how should i do it? I dont know how to > manually modify the sequence file (which will be used by modeller)
The sequence file is just a plain text file, which you can create in any text editor.
Ben Webb, Modeller Caretaker