On 04/24/2012 10:43 AM, Isaure Chauvot de Beauchêne wrote: > one of the PTR is changed in ASP in my results, > because Modeller change the alignment I gave in my .ali file.
Modeller does not change the alignment file - it simply reads in what you gave it.
> read_te_291E> Sequence difference between alignment and pdb : > x (mismatch at alignment position 120) > Alignment ETNE.MDMK > PDB ETNEMDMK > Match ***** > Alignment residue type 11 (M, MET) does not match pdb > residue type 3 (D, ASP), > for align code 2iuh (atom file 2iuh), pdb residue number "206", chain "B"
The alignment here matches what you have in your alignment file. But note that it doesn't match what's in the PDB file. Maybe you forgot to set env.io.hetatm=True? If so, Modeller will strip any HETATMs out of your PDB file.
Ben Webb, Modeller Caretaker