I need help

[A.Romani AT leonardo.biomed.unipr.it]

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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 : A.Romani AT leonardo.biomed.unipr.it
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