Re: [modeller_usage] problem in modelling

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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