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I'm able to perform the basics of building, but now I've few questions to improve my model.
I'built the model with the top script below :
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INCLUDE # Include the predefined TOP routines
SET ALNFILE = 'alignment.ali' # alignment filename
SET SEQUENCE = 'my_sequence'
SET LIBRARY_SCHEDULE = 1
SET MD_LEVEL = 'refine1'
SET FINAL_MALIGN3D = 1
SET REPEAT_OPTIMIZATION = 5
SET RSTRS_REFINED = 5
SET MD_RETURN = 'MINIMAL'
SET KNOWNS = 'knows1' 'knows2' 'knows3' # codes of the templates
SET ATOM_FILES_DIRECTORY = '/disk2/modeller4/examples' # directories for input atom files
SET STARTING_MODEL= 1 # index of the first model
SET ENDING_MODEL = 20 # index of the last model
# (determines how many models to calculate)
CALL ROUTINE = 'model' # do homology modelling
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With this script am I sure to build an accurate model? Are there other stuff that I can do to improve my
model? How can I transfer the heteroatoms from template to model?
Thanking in advance
Your faithfully
Antonello Romani
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Antonello Romani
Istituto di Patologia Generale
Plesso Biotecnologico Integrato
Universita' degli Studi di Parma
via Volturno 39
43100 Parma
Tel. +39 521 903 751
Fax. +39 521 903 742
E-mail :
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