[modeller_usage] Re: Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1)
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Subject: [modeller_usage] Re: Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1)
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Date: Mon, 31 Mar 2025 20:14:19 +0000
Hi Fred,
I think you'll need to change the name of your known to match what's in your .pir alignment file, and make them match between the header lines. Try leaving off the .pdb extension
>P1;6KG7
structureX:6KG7:8:A ... etc
see
https://salilab.org/modeller/10.6/manual/node501.html#alignmentformat
Jed Goldstone
Woods Hole Oceanographic Institution