My name is Amanda and I`ve read that changing modeller seed helps to achieve a better model. In my top file, where can I put the new comand? And how to write it? I know that the number must be negative. Sorry for the stupid question. Thank you in advance!
INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'novo_alinhamento.ali' # alignment filename SET KNOWNS = '1MDY' '1NKP' '2QL2' '1HLO' # codes of the templates SET SEQUENCE = 'twist1' # code of the target SET STARTING_MODEL = 1 SET ENDING_MODEL = 100 CALL ROUTINE = 'model' # do homology modelling
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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?
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