Dear Ben,
I apologize for not understanding correctly here. Currently, I am following the .PIR file setup I see in the tutorial (https://salilab.org/modeller/wiki/Missing%20residues):
>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.orgmailto: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 -- modeller-care@salilab.orgmailto:modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage