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

> From: Dany Naranjo Feliciano dany@censa.edu.cu > 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