I edited the alignment file (SF3B1-Mult.ali) and would like to generate a protein model.
Edited the templates sequence accordingly to start from position 610-1198.
It is however, I keep getting the error message 'sequence difference between alignment and PDB'.
Being the first time Modeller user, would anyone be kind enough to guide me as to how I should rectify the problem.
Hereby I attached the alignment file along with this email.
On 09/04/2015 08:29 PM, Wong Li Zhe wrote: > It is however, I keep getting the error message 'sequence difference > between alignment and PDB'.
Well... the sequence in your alignment does not match that from the PDB. The Modeller output should show the two sequences, so it should be obvious where the difference is.
> Hereby I attached the alignment file along with this email.
Nobody is going to be able to tell the difference between the alignment and the PDB if you only attach the alignment - they'd need to see the PDB as well.
Ben Webb, Modeller Caretaker