On 4/5/21 5:42 PM, Steven Truong wrote: > 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?
The template is the known structure, i.e. the PDB file, 1qg8 in the example.
> >P1;6z43 > structureM:6z43:27:A:+3600:C:::-1.00:-1.00 > AYTNSFTR*-*VYYPDKVFRSSVLHSTQDLFLPFFSNVTWFH--------------NPVLPF > NDGVYFAST
Well, this simply isn't correct. The "missing" glycine here isn't missing in the 6z43 PDB file - it is there (residue 35 in chain A). What are you trying to accomplish here?
Ben Webb, Modeller Caretaker