Amanda Moraes wrote:
> My name is Amanda and I`ve read that changing modeller seed helps to
> achieve a better model.
It will give you a *different* model, not necessarily a "better" one.
(For regular homology modeling runs, setting the random seed is
essentially equivalent to setting ENDING_MODEL to build multiple
different models.) The most obvious way to get a better model (given the
same starting alignment and restraints) is to build multiple different
models and then pick the best one using some assessment method.
> In my top file, where can I put the new comand?
If you're using TOP, you can put it anywhere in the script after the
INCLUDE but before the CALL.
> And how to write it?
For example:
SET RAND_SEED = -4000
However, TOP is very old - you'd be better off using a Python script
with modern versions of Modeller. The equivalent Python script for your
modeling run (complete with a different random seed) would be:
from modeller import *
from modeller.automodel import *
log.verbose()
env = environ(rand_seed=-4000)
a = automodel(env, alnfile='novo_alinhamento.ali',
knowns=('1MDY', '1NKP', '2QL2', '1HLO'),
sequence='twist1')
a.starting_model = 1
a.ending_model = 100
a.make()
Ben Webb, Modeller Caretaker
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