Re: [modeller_usage] problem with ligand modelling

[Modeller Caretaker <>]

sanjay singh wrote:
...
> my alignment looks like this
>
>  >P1;1iax
> structureX:1iax:11    :A :438  :B :ferredoxin:Azotobacter vinelandii: 
> 1.90: 0.19
> ILSKLATNE-----SPYFDGWKAYDSDPFHPLKNPNGVIQMGLAENQLCLDLIEDWIKRN
//
> NAGLFCWMDLRPLLRESTFDSEMSLWRVIINDVKLNVSPGSSFECQEPGWFRVCFANMDD
> GTVDIALARIRRFVGVEK/..*
...
> read_te_290E> Number of residues in the alignment and  pdb files are 
> different:      836      834
>               For alignment entry:        1  1iax
>                                 x  (mismatch at alignment position    835)
> Alignment  VDIALARIRRFVGVEK..                                     
>       PDB  VDIALARIRRFVGVEK                                       
>     Match  ****************
>
>   Please check your alignment file header to be sure you correctly specified
>   the starting and ending residue numbers and chains. The alignment sequence
>   must match that from the atom file exactly.

You should follow the advice in the error message, and check your 
alignment file header. Your header tells Modeller to read residues 11:A 
through 438:B from your PDB file, so it's not going to read the HETATMs, 
which come after 438:B. Fix your alignment header.

BTW, your PDB file contains 4 HETAMs (two SO4 and two PLP) but your 
alignment sequence contains only two.

	Ben Webb, Modeller Caretaker
--
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