Hello,

I have a problem trying to use external alignment (from Clustal Omega, converted to PIR format). However, Modeller refuses to read the PDB template. After several rounds of iterative correction, I specified only the residues and numbers actually present in the PDB file in alignment: >P1;5u09A structure:5u09A: 100 :A:+478 :A:::: ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------E NFMDIECFMV LNPSQQLAIA VLSLTLGTFT VLENLLVLCV ILHSRSLRCR

But I get the following error: read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 11) Alignment .....E.NFMDIECFMV.LNPSQQLAIA.VLSLTLGTFT.VLENLLVLCV.ILHSRSLRC PDB IECFMVLNPSQQLAIAVLSLTLGTFTVLENLLVLCVILHSRSLRCRPSYHFIGSLAVADL Match ***** ** ** * * * ** Alignment residue type 4 (E, GLU) does not match pdb residue type 18 (V, VAL), for align code 5u09A (atom file 5u09A), pdb residue number "110", chain "A"

That is, it somehow skips the first 5 residues from the PDB but adds 5 dots to the alignment sequence, and then (unsurprisingly) everything breaks =( What is wrong?

Thank you in advance Eugene