I try to make models from a template, with constraints (Helix) and a
randomization of the coordinates for each models. I set deviation to 4.0
but MODELLER dont use it. A part of my script:
What do you mean by "MODELLER dont use it"? Your script looks fine to
me, but the default for deviation is 4.0 anyway, so explicitly setting
it to 4.0 won't make any difference.