In the interests of appearing to make progress, I dropped the alignment of which I wrote an hour or so ago from the mulitple alignments considered. Now I have another sequence difference issue with 1x06.pdb. This is how it aligns with my sequence [clustal w server pir output, with line 2 edited by hand]

:>P1;1x06
structureX:1x06:12:A:240:A:UPP       :Erischeria coli   : :
-------------------------------------MMLSATQPLSEKL
PAHGCR-HVAIIMDGNGRWAKKQGK-IRAFGHKAGAKSVRRAVSFAANNG
IEALTLYAFSSENWNRPAQEVSALMELFVWALD---SEVKSLHRHNVRLR
IIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQL
AEKVQQ----GNLQPDQIDEEMLNQHVCMHELA-----------------
-PVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAF
ANRERRFGGTEPGDETA

I checked it myself against the original fasta sequence deposited in the pdb & can't find any differences. The only missing residues are those below 12 & above 240. I scrolled through the pdb file & can't find any residues missing that might not have been noted in the header. Is there a way to get more detailed information on the problem region, or a tool to check fasta sequences against a pdb file?

Thanks!
Irene

The relevant end of the error log is:

Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:      3879167    3788.249     3.699
read_te_291E> Sequence difference between alignment and  pdb :
                  x  (mismatch at alignment position      1)
 Alignment        MMLSATQPLSEKLPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSF
       PDB        KLPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTL
     Match                          *             *   *         *     *
  Alignment residue type   11 (M, MET) does not match pdb
  residue type    9 (K, LYS),
  for align code 1x06 (atom file 1x06), pdb residue number "12", chain "A"

  Please check your alignment file header to be sure you correctly specified
  the starting and ending residue numbers and chains. The alignment sequence
  must match that from the atom file exactly.

  Another possibility is that some residues in the atom file are missing,
  perhaps because they could not be resolved experimentally. (Note that Modeller
  reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
  In this case, simply replace the section of your alignment corresponding
  to these missing residues with gaps.
read_te_288W> Protein not accepted:        3  1x06