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