rathankar rao wrote: > am having a problem in modelling a protein, plz help ... > rdabrk__290E> Number of residues in the alignment and pdb files are different: 43 33 > For alignment entry: 5
Just like Modeller is telling you, your alignment has a different number of residues in it than the PDB file does. The 5th entry in your alignment is 1krh, which your alignment gives as:
StructureX:1KRH :295:B: 327:B :Oxidored:uk4: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------WLNGGEVDV--YLCGPVPMVE-AVRSWLDTQGIQPANFL FEKFSAN------------------------------------------------------ ------------------------------------------------------*
You have told Modeller to read residues 295 through 327 from the PDB file, i.e. 33 residues. But your alignment has 43 residues in it. You need to either remove 10 residues from the alignment, or change either 295 or 327 in the header.
Ben Webb, Modeller Caretaker