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():
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.