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