On 1/4/12 6:24 PM, Ashish Runthala wrote: > Is there any way to incorporate CSA (Conformational Space > Annealing)alignment approach in Salign_multiple_struc.py? Or is there > any similar script in MODELlER which computes such alignments?

While it is possible to change the distance or similarity matrix used by SALIGN, it is not possible to change the method it uses (dynamic programming) to generate the alignment. If you wanted to do CSA, you would need to use a different package or implement the algorithm yourself (there is of course no requirement that you generate modeling alignments for Modeller using Modeller itself).

Ben Webb, Modeller Caretaker