Re: [modeller_usage] SequenceMismatchError when adding missing residues in LoopModel()

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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