On 8/26/16 1:58 PM, Maryam Faridounnia wrote:

I'm trying to get the format right for a multiple alignment, I did in
HHpred server to use as input to modeller. I don't understand the error
messages.

I only see one error message:

_modeller.SequenceMismatchError: read_te_291E> Sequence difference
between alignment and  pdb :

I'm not sure how to state the error any more clearly than it is already... but the sequence in your alignment has to match the sequence in the PDB file. So you have to change one or the other (usually the alignment) so that they match. If you look in the Modeller log file it will show you exactly where the mismatch occurred. Usually it's just a single residue mutation or a short insertion.

        Ben Webb, Modeller Caretaker
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