[modeller_usage] To use separate templates for different region of a protein

[Shirley Li <li19104 AT yahoo.com>]

Dear All,
 
 With MODELLER, I wonder if it is possible to use different template(s) for different region of one target protein.  For example,  One protein has domain 1, 2 and 3.  I would like to construct a complete model of this protein,  with templates A and B for domain 1, templates C,D,and E for domain 3,  and domain 2 already has coordinates/structure, which need to be preserved in the complete model.
 
 Is there any way to do the above?  If so, how?  I tried to use the "inifile" feature and use the existing coordinate file of domain 2 as "inifile".  while I got error message of " Atom index is out of range (iatm,natm)".
 
 Any help/information will be very much appreciated.
 
 Shirley

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