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Ensure you enter your valid MODELLER key via the BioSerf tab.

You input looks like it may be a multiple sequence alignment, please ensure it is in valid fasta format and that all sequences are the same length

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Metsite will only analyse one chain in the PDB file at a time

There must be at least 2 chains in your PDB file.

MakeTDB will only analyse single chain PDB files.

Memembed will only process membrane proteins.