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Article ID: 1099 - Last Modified: January 21, 2011

Prime gives a warning that the query sequence is invalid and must be fixed before continuing in the homology modeling workflow:

"Warning: the sequence is invalid at position 1: you must fix this before you continue"

What does this mean?

Modified residues in query sequences are named X in the sequence. Prime is not able to handle query sequences with modified residues, so they will have to be fixed before going through the homology modeling workflow. Depending on what you know about the system, you might want to change the X either to a closely related residue or maybe just to a GLY as a placeholder.

Keywords: modified residue, query sequence

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