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Dear Ben and Modeller Mailing List,
Hello, I was hoping to get some help on an error I get when trying to add missing residues to a structure using the AutoModel/LoopModel classes.
The error looks like:
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"
When I check my alignment file, I can begin to see what’s going on. Here is the first entry of the alignment file:
>P1;6z43
structureM:structure_aligned:27:A:+3600:C:::-1.00:-1.00
--------------------------AYTNSFTR-VYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFH--------------NPVLPFNDGVYFAST
>P1;6z43_fill
sequence:6z43_fill:.:.:.:.::::
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFAST
It appears that Modeller does not recognize the dashes “-“ as actual missing residues. Instead, it appears to read the alignment as
NSFTR()V…, rather than NSFTRG. However, isn’t the dash supposed to signal AutoModel/LoopModel to treat that as a missing residue to fill?
Thank you for your help!
Best wishes,
Steven Truong
Cambridge University
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