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Re: [modeller_usage] [Fwd: Re: The models miss the 40 first aa of the sequence]

From: 	Dany Naranjo Feliciano <>
When I visualized the models using vmd, I can't see the first 40aa of
the sequence.
You should first check the generated PDB files with a text editor, to make sure the first 40aa are actually there. If they are, then either VMD is doing something weird (try a different PDB viewer) or the PDB file is corrupt in some way, which should be obvious from a visual inspection.
If they are not there, it's probably because you didn't ask Modeller to build those residues in the first place. Check your alignment. 

	Ben Webb, Modeller Caretaker
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