-------- 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 : _____________________________________________

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 _____________________________________________________________________________________

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

________________________________ 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@leonardo.biomed.unipr.it _______________________________