Hello, 

I'm using thos PIR file:
>P1;2ks9
structureX:2ks9:1 :A :364 : ::::
MDNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWIILAHKRMRTVTNYFLVNLAFAEAS
MAAFNTVVNFTYAVHN-EWYYGLFYCKFHNFFPIAAVFASIYSMTAVAFDRYMAIIHPLQPR--LSATATKVVICVIWVL
ALLLAFPQGYYSTTETM-PSRVVCMIEWPEHP---------NKIYEKVYHICVTVLIYFLPLLVIGYAYTVVGITLWASE
IPGDSSDRYHEQVSAKRKVVKMMIVVVCTFAICWLPFHIFFLLPYINPDLYLKK---FIQQVYLAIMWLAMSSTMYNPII
YCCLNDRFRLGFKHAFRCCPFISAGDYEGLEMKSTRYLQTQGSVYKVSR*

>P1;FPR1
sequence:FPR1:1 : :350 : ::::
METNSSL------PTNISGGTPAVSAGYLFLDIITYLVFAVTFVLGVLGNGLVIWVAGFRMT-HTVTTISYLNLAVADFC
F-TSTLPFFMVRKAMGGHWPFGWFLCKFVFTIVDINLFGSVFLIALIALDRCVCVLHPVWTQNHRTVSLAKKVIIGPWVM
ALLLTLPVIIRVTTVPGKTGTVACTFNFSPWTNDPKERINVAVAMLTVRGIIRFIIGFSAPMSIVAVSYGLIATKIHKQG
------------LIKSSRPLRVLSFVAAAFFLCWSPYQVVALIATVRIRELLQGMYKEIGIAVDVTSALAFFNSCLNPML
YVFMGQDFRERLIHALPASLERALTEDSTQTSDTATNSTLPSAEVELQA*

***The file 2ks9.pdb is exactly as I downloaded it from RCSB.. then I'm running the script:
from modeller import *
from modeller.automodel import *

env = environ()
a = automodel(env, alnfile='alnPrev.pir',
              knowns='2ks9', sequence='FPR1',
              assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 1
a.make()

I can't seem to understand why do I get the following error:
rdpdb___303E> No atoms were read from the specified input PDB file, since the
              starting residue number and/or chain id in MODEL_SEGMENT (or
              the alignment file header) was not found;
              requested starting position: residue number " 1", chain " A";
              atom file name:  2ks9.pdb
read_te_288W> Protein not accepted:        1  2ks9

It seems like it can't find residue number 1 but I think I can see it.. And when I'm changing the PIR file in the structure line from 1 to first I get the following error:
read_te_291E> Sequence difference between alignment and  pdb :
                  x  (mismatch at alignment position      1)
 Alignment        MDNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWI
       PDB        DNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWII
     Match                                           **     *   *   **   *
  Alignment residue type   11 (M, MET) does not match pdb
  residue type    3 (D, ASP),
  for align code 2ks9 (atom file 2ks9), pdb residue number "2", 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:        1  2ks9

What am I missing?

The beggining of the ATOM part in the PDB file:
MODEL        1                                                                  
ATOM      1  N   ASP A   2     -17.531 -22.009 -19.661  1.00 97.08           N  
ATOM      2  CA  ASP A   2     -17.664 -21.563 -18.309  1.00 97.08           C  
ATOM      3  C   ASP A   2     -17.647 -20.070 -18.302  1.00 97.08           C  
ATOM      4  O   ASP A   2     -18.309 -19.432 -17.485  1.00 97.08           O  
ATOM      5  CB  ASP A   2     -16.522 -22.041 -17.395  1.00 97.08           C  
ATOM      6  CG  ASP A   2     -15.222 -21.430 -17.892  1.00 97.08           C  
ATOM      7  OD1 ASP A   2     -15.049 -21.341 -19.136  1.00 97.08           O  
ATOM      8  OD2 ASP A   2     -14.389 -21.037 -17.033  1.00 97.08           O  
ATOM      9  H   ASP A   2     -16.684 -22.502 -19.945  1.00  0.00           H  
ATOM     10  HA  ASP A   2     -18.637 -21.921 -17.898  1.00  0.00           H  
ATOM     11  HB2 ASP A   2     -16.714 -21.822 -16.319  1.00  0.00           H  
ATOM     12  HB3 ASP A   2     -16.471 -23.152 -17.318  1.00  0.00           H  
ATOM     13  N   ASN A   3     -16.889 -19.477 -19.238  1.00123.41           N  

Thanks, 
Yael.