|
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 |