Re: [modeller_usage] Enc: ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 4) = G8EW14.fasta

[Modeller Caretaker <>]

On 8/6/15 7:52 AM, Samuel Silva Pita wrote:
> I'd tried to generate 5 models from Modeller v9.15 trough my
> model-multi.py script [1] and the program gave me this error:
...
> _modeller.ModellerError: read_al_373E> Protein specified in
> ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(
> 4) =  G8EW14.fasta

You asked Modeller to read the sequence called "G8EW14.fasta" from your 
alignment file by saying sequence=('G8EW14.fasta') in your Python script:

> # Modelling 'sequence' with file.ali
> a = automodel(env, alnfile='CpLANcab.ali',
>                knowns=('4LXJ','4K0F','4WMZ'),
>                sequence=('G8EW14.fasta'),

But you don't have a sequence by that name in your alignment file:

> > P1;G8EW14
> sequence:G8EW14.fasta:::::::0.00: 0.00

Note that the G8EW14.fasta on the second line is the name of the PDB 
file that Modeller will read the structure from (see 
http://salilab.org/modeller/9.15/manual/node494.html, field 2). The name 
of the sequence is the part after P1;, i.e. "G8EW14". Modify your Python 
script accordingly.

	Ben Webb, Modeller Caretaker
--
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