On 4/5/21 5:05 PM, Steven Truong wrote:
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"
The template sequence in the alignment has to match exactly the sequence of ATOM/HETATM records in the PDB file. You are missing a glycine.
It appears that Modeller does not recognize the dashes “-“ as actual missing residues.
This is an alignment. Dashes have no meaning except to align residues in one sequence with those in another. Obviously Modeller ignores them when reading the PDB file, as there are no "-" residues there.
However, isn’t the dash supposed to signal AutoModel/LoopModel to treat that as a missing residue to fill?
No. A residue in your target sequence that isn't aligned with a residue in the template sequence (e.g. it lines up with a gap or chain break, or extends past the end of the template sequence) will be constructed from first principles.
If you have a residue in your template which for some reason you don't want in your target, align it with a gap in the target.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage