Re: [modeller_usage] Loop Modeling using only part of a PDB file

Robert Selwyne wrote: > Residues from PHE 1223 to LEU 1245 are missing from PDB:2RFN. I want > to use ONLY the residues from 382 to 406 in my template sequence > PDB:3LCK for loop modelling. Remaining part of the residues in the > target shouldnot be disturbed. > > (2RFN) Target : PHE 1223 to LEU 1245 (24 residues) > (3LCK) Template : ASP 382 to TRP 406 (24 residues) > > Could you please tell me how to model this?

This is not what Modeller calls "loop modeling"; that is modeling a region that has no template. To do what you're asking you should use something similar to http://salilab.org/modeller/9v7/manual/node23.html

Ben Webb, Modeller Caretaker