Loop Modeling using only part of a PDB file
Dear Modeller Users 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?
Regards Robert
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
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Modeller Caretaker -
Robert Selwyne