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



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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