>P1;1qg8
structureX:1qg8:   2 :A: 256 :A:undefined:undefined:-1.00:-1.00
PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR
YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLN---DIVKETVRPAAQVTW
NAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYIT---------
-----EFVRNLPPQRNCRELRESLKKLGMG*
>P1;1qg8_fill
sequence:::::::::
PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR
YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTW
NAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLF
ELEKNEFVRNLPPQRNCRELRESLKKLGMG*

I think I have the template sequence alignment matching exactly to the PDB file, in the same way the second entry “1qg8_fill” has a full sequence. However, I am indicating missing residues with “1qg8.” Should I fill in those dashes with missing residues? I’m likely misunderstanding how AutoModel/LoopModel works then. When you refer to “template sequence,” is that “1qg8” or “1qg8_fill” in the align.pir file on the tutorial?

Pasting my version of align.pir again for reference (I’ve bolded/colored red the glycine Modeller is detecting an error on):

>P1;6z43

structureM:6z43:27:A:+3600:C:::-1.00:-1.00

AYTNSFTR-VYYPDKVFRSSVLHSTQDLFLPFFSNVTWFH--------------NPVLPF

NDGVYFAST

[…]

>P1;6z43_fill

sequence:6z43_fill::::::::

AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPF

NDGVYFAST

Thank you for your help again! Apologies for the misunderstanding.

Best wishes,

Steven Truong

On Apr 5, 2021, at 7:33 PM, Modeller Caretaker <modeller-care@salilab.org> wrote:

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
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