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 sdt45@cam.ac.ukmailto:sdt45@cam.ac.uk Cambridge University