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
|