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
