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Sequences must be amino-acid sequences with no gaps(-) and no ambiguous residues(B, O, U, X, Z).
Multiple chains may be included, but may make template selection more difficult.
A header line is not required if only submitting a sequence for a single chain.
Specially-formatted header lines are not required in Auto mode. Chains in the output will be named in this order: "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz123456789"

Query sequences must have FASTA headers of the format query[chain_id]. Example: queryD
Queries must be amino-acid sequences with no gaps(-) and no ambiguous residues(B, O, U, X, Z).
Every query entry in the FASTA file must have a corresponding template alignment.
Template alignments must have FASTA headers of the format template[chain_id]. Example: templateD
Template alignments may contain gaps(-), but may not contain ambiguous residues(B, O, U, X, Z).
Terminal gaps must be less than 65 residues. Internal gaps must be less than 96 residues.
Structure gaps must have at least 5 residues on each side of the gap to be used as anchors.
Template structure may be in any of these formats: .pdb, .cif, .cif.gz
Template structure must have the same number of chains as pairs of query/template entries in the FASTA file.
Only non-ambiguous residues with backbone atoms(N, CA, C, O) will be considered. Residues with incomplete backbone will be removed, and the resulting gaps will be filled during model assembly.
If a problem is found with the submitted alignment FASTA an automated re-alignment process will be attempted. In this case the Results page will show the alignment that was ultimately used.

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