Hello, I was hoping to get some help on an error I get when trying to add missing residues to a structure using the AutoModel/LoopModel classes.

The error looks like:

                  x  (mismatch at alignment position      9)
 Alignment   NSFTRVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHNPVLPFNDGVYFASTKSNIIRGWI 
       PDB   NSFTRGVYYPDKVFRSSVL.STQDLFLPFFSNVTWF.AI.VSGTNGTKRFDNPVLPFNDG 
     Match   *****  *       *            *
  Alignment residue type   18 (V, VAL) does not match pdb
  residue type    6 (G, GLY),
  for align code 6z43 (atom file structure_aligned), pdb residue number "          35", chain "A"

When I check my alignment file, I can begin to see what’s going on.  Here is the first entry of the alignment file:

It appears that Modeller does not recognize the dashes “-“ as actual missing residues.  Instead, it appears to read the alignment as NSFTR()V…, rather than NSFTRG.  However, isn’t the dash supposed to signal AutoModel/LoopModel to treat that as a missing residue to fill? 

Thank you for your help!

Best wishes,

Steven Truong

Cambridge University