Re: [modeller_usage] "Structure not read in" error

[Modeller Caretaker <>]

Omid Khalouei wrote:
> This is the end of my log-file:
>
> ####################################################
> Read the alignment from file       : 1ZPA-1A8GA.ali
> Total number of alignment positions:    99
>
>  #  Code        #_Res #_Segm PDB_code    Name
> ------------------------------------------------------------------------------- 
>
>  1      1A8GA      99      1       1A8GA Comeon
>  2       1ZPA      99      1        1ZPA Comeon
> runcmd______> alignment.check()
>
> check_a_343_> >> BEGINNING OF COMMAND
> openf5__224_> Open       11  OLD  SEQUENTIAL  
> .\examples\atom_files\1A8GA.pdb
> rdpdb___303E> No atoms were read from the specified input PDB file, 
> since the
>              starting residue number and/or chain id in MODEL_SEGMENT (or
>              the alignment file header) was not found;
>              requested starting position:  1A    :
> rdabrk__288W> Protein not accepted:        1
> check_a_337E> Structure not read in:        1
> ####################################################
>
> and here's my alignment file, I followed what I saw on the link that you 
> sent me.
>
> > P1;1A8GA
>
> structureX:1A8GA:1    : :99  : :HIV1 PR: : 1.90: 0.19
> PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD
> QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF*
>
> > P1;1ZPA
>
> sequence:1ZPA:1     : :99  :  :HIV1 PR: : 1.90: 0.19
> PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD
> QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF*

Like I said, your alignment file is incorrect. Furthermore, I can't see 
how that alignment file could generate that error - are you sure that's 
the one you're using? The error message says that your alignment file is 
requesting to read the sequence starting at residue '1A' in a chain with 
no identifier, while the alignment file you've posted requests to read 
starting from residue '1' in a chain with no identifier. What I suspect 
you actually want to do is read from residue '1' in chain 'A'. So your 
alignment header would look something like
structureX:1A8GA:1    :A:99  :A:HIV1 PR: : 1.90: 0.19

	Ben Webb, Modeller Caretaker
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