Hi,
I need some help with optimization. I am confused what to do.
This is what i have done so far. On the first instance i used the scrip one to build the models. As i was not satisfied with the structural quality of the models, i used the second script below where i included a refinement command. Even then i couldn't get good models. So, i tried to a optimization script (third), to see if i can build the models by iterative optimization. But that script just kept on failing. So, I am not sure what the problem is..
*One*: This one does not have the refine command
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = '2BCK.pir' # alignment filename SET KNOWNS = '2BCK' # codes of the templates SET SEQUENCE = 'MesoA1' # code of the target # SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 3 # index of the last model # (determines how many models to calculate) SET HETATM_IO = on CALL ROUTINE = 'model' # do homology modelling STOP -------------------------------------------------------------------------------------------------------------------------------------- * * *Two*: This has the refine command INCLUDE # Include the predefined TOP routines
SET ALNFILE = '2BCK.pir' # alignment filename SET KNOWNS = '1BCK' # codes of the templates SET SEQUENCE = 'MesoA1' # code of the target SET ATOM_FILES_DIRECTORY = './:../../atom_files' # dirs for input atom files SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 SET DEVIATION = 6.0 SET MD_LEVEL = 'refine_2' #SET OUTPUT_CONTROL = 1 1 1 1 1 SET OUTPUT_CONTROL = 1 0 0 1 0
CALL ROUTINE = 'model' # do homology modelling --------------------------------------------------------------------------------------------------------------------------------------- * * *Third*: INCLUDE SET ALIGNMENT_FILE = '2BCK.pir', KNOWNS='2BCK', SEQUENCE='MesoA1' # Very thorough VTFM optimization: SET LIBRARY_SCHEDULE = 1, MAX_VAR_ITERATIONS = 300 # Very thorough MD optimization: SET MD_LEVEL = 'refine1' # Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6 SET REPEAT_OPTIMIZATION = 3, MAX_MOLPDF = 1E6 CALL ROUTINE = 'model' ---------------------------------------------------------------------------------------------------------------------------------------
I will appreciate if some one can help me.
thanks in advance!!
Harish
On 5/7/10 7:42 PM, Harish Reddy wrote: > I need some help with optimization. I am confused what to do.
Your best option is to build more models, assess them, and choose the best one (or change your alignment/template if none of the models are acceptable). You would be better off doing this with Python scripts, as the old Modeller TOP scripts are no longer documented or supported.
> On the first instance i used the scrip one to build the models. As i was > not satisfied with the structural quality of the models, i used the > second script below where i included a refinement command. Even then i > couldn't get good models. So, i tried to a optimization script (third)
Actually, all your scripts do the same thing - they call the regular modeling procedure. You have changed the amount of refinement and the optimization parameters slightly, but this does not usually have a large influence on the output models.
> But that > script just kept on failing. So, I am not sure what the problem is..
I can't tell what the problem is either! What do you mean by "the script just kept on failing" ?
Ben Webb, Modeller Caretaker
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Harish Reddy -
Modeller Caretaker