On 3/9/10 7:18 AM, Knut J Bjuland wrote: > I used multiple alignment with protein sequence to get a better > alignment with a template. Is this a good practice. What are the > recommende settings in salign to get the best possible alignment.

Generally, multiple templates have been shown to yield better models than single templates, but you do have to be more careful in the generation of your alignment to avoid conflicts in the information implied by each template.

Assuming you want a structural alignment of your templates, you will get the best results from SALIGN using iterative_structural_align(): http://salilab.org/modeller/9v7/manual/node407.html

After that, you can align the block of structures with the target sequence using a sequence-structure alignment and align_block set to the number of templates.

Ben Webb, Modeller Caretaker