Dave Roe wrote:
I'm receiving the following error on linux with Modeller 9.2:
_modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = mod2hg42
Here's the alignment line from my python file:
aln = alignment(env, file='mod2hg42.fa', align_codes=('mod2hg42'))
Your alignment file looks like a FASTA file, and you haven't specified 'alignment_format' when reading it in, so Modeller will treat it as a PIR file by default. Since there is no valid PIR sequence in that file, it won't find your sequence.
Add alignment_format='FASTA' when reading your alignment, or (better) switch your alignment to PIR format, and everything should work.
Ben Webb, Modeller Caretaker
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