I'm trying to get the format right for a multiple alignment  I did with a Clustal W server to use as input to modeller. I don't understand the error message; it probably means I don't understand the numbering convention. My sequence has 290 residues & ends up with 316 characters due to alignment gaps. I get exactly the same error message whether I use 290 or 316 as the end residue. Below are various bits of information that might be helpful in debugging what I'm doing.

Thanks for your help!
Irene Newhouse

***The input python script:
[newhoir@localhost rubber]$ cat  mod-rubber1.py
# Homology modeling with multiple templates
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = ['.', '/home/newhoir/rubber/atom_files']

a = automodel(env,
              alnfile  = 'multi.ali', # alignment filename
              knowns   = ('2d2r', '1ueh', '2vg3', '1f75', '2vg0'),     # codes of the templates
              sequence = '2cpt')               # code of the target
a.starting_model= 1                 # index of the first model
a.ending_model  = 5                 # index of the last model
                                    # (determines how many models to calculate)
a.make()                            # do the actual homology modeling

***The run command:
mod9v8 mod-rubber1.py

***atom_files:
ls -l /home/newhoir/rubber/atom_files
total 2640
-rw-rw-r-- 1 newhoir newhoir 324891 Nov 16 11:17 1f75.pdb
-rw-rw-r-- 1 newhoir newhoir 405810 Nov 16 11:18 1ueh.pdb
-rw-rw-r-- 1 newhoir newhoir 372276 Nov 16 11:19 2d2r.pdb
-rw-rw-r-- 1 newhoir newhoir 707778 Nov 16 11:18 2vg0.pdb
-rw-rw-r-- 1 newhoir newhoir 862326 Nov 16 11:18 2vg3.pdb

*** input file multi.ali

>P1;2d2r
structureX:2d2r:A:3:A:227:UPP       :Helicobacter pylori:  :
---------------------------------------MLSATQPLSEKLDST-LKHLAIIMDGNGRWAKLKNK
-ARAYGHKKGVKTLKDITIWCANHKLECLTLYAFSTENWKRPKSEVDFLMKMLKKYLK---DERSTYLDNNIRFR
AIGDLEGFSKELRDTILQLENDTRHFKDFTQVLALNYGSKNELSRAFKSLLESPPS-NISLLE------------
---------SLENEISNRLDTRNLPEVDLLLRTGGEMRLSNFLLWQSSYAELFFTPILWPDFTPKDLENIISDFY
KRVRKFGELKA-----*

>P1;1ueh
structureX:1ueh:A:13:A:240 :UPP       :Erischeria coli   : : 
--------------------------------------MMLSATQPLSEKLPAHGCRHVAIIMDGNGRWAKKQGK
-IRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALD---SEVKSLHRHNVRLR
IIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQ------------
---------IDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFA
NRERRFGGTEPGDETA*

>P1;2vg3
structureX:2vg3:A:13:A:296:rv2361c decaprenyl PP:M. tuberculosis: :
FPQLPPAPDDYPTFPDTSTWPVVFPELPAAPYGGPCRPPQHTSKAAAPRIPADRLPNHVAIVMDGNGRWATQRGL
-ARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFSTENWKRSPEEVRFLMGFNRDVVR---RRRDTLKKLGVRIR
WVGSRPRLWRSVINELAVAEEMTKSNDVITINYCVNYGGRTEITEATREIAREVAAGRLNPER------------
---------ITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYAEYIFQDKLWPDYDRRDLWAACEEYA
SRTRRFGSA-------*

>P1;1f75
structureX:1f75:A:14:A:242:UPP         :Micrococcus luteus: :
-----------------------------------MFPIKKRKAIKNNNINAAQIPKHIAIIMDGNGRWAKQKKM
-PRIKGHYEGMQTVRKITRYASDLGVKYLTLYAFSTENWSRPKDEVNYLMKLPGDFLN---TFLPELIEKNVKVE
TIGFIDDLPDHTKKAVLEAKEKTKHNTGLTLVFALNYGGRKEIISAVQLIAERYKSGEISLDE------------
---------ISETHFNEYLFTANMPDPELLIRTSGEERLSNFLIWQCSYSEFVFIDEFWPDFNEESLAQCISIYQ
---------------*

>P1;2vg0
structureX:2vg0:A:30:A:256:Rv 1086 farnesyl PP:M. tuberculosis: :
-----------------------------------------------------DLPRHIAVLCDGNRRWARSAGY
DDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVE---EICAPANHWSVRT-
-VGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDA--------
---------VTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYS
AR--------------*

>P1;2cpt
sequence:2cpt::1: :316:rubber c-prenylxferase:Hevea brasiliensis: :
-----------------------MELYTGERPSVFRLLGKYMRKGLYGILTQGPIPTHLAFILDGNRRFAKKHKL
-PEGGGHKAGFLALLNVLTYCYELGVKYATIYAFSIDNFRRKPHEVQYVMDLMLEKIEGMIMEESIINAYDICVR
FVGNLKLLSEPVKTAADKIMRATANNSKCVLLIAVCYTSTDEIVHAVEESSELNSNEVCNNQELEEANATGSSTV
IQTENMESYSGIKLVDLEKNTYINPYPDVLIRTSGETRLSNYLLWQTTNCILYSPHALWPEIGLRHVVWAVINCQ
RHYSYLEKHKEYLK--*

***The runtime messages:
[newhoir@localhost rubber]$ ./r
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "mod-rubber1.py", line 18, in ?
    a.make()                            # do the actual homology modeling
  File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line 98,
in make
    self.homcsr(exit_stage)
  File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line
424, in homcsr
    self.check_alignment(aln)
  File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line
406, in check_alignment
    aln.check()
  File "/usr/lib/modeller9v8/modlib/modeller/alignment.py", line 200, in check
    self.check_structure_structure(io=io)
  File "/usr/lib/modeller9v8/modlib/modeller/alignment.py", line 209, in
check_structure_structure
    return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.ModellerError: 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 " A", chain " 3"; atom file name:
/home/newhoir/rubber/atom_files/2d2r.pdb
[newhoir@localhost rubber]$

***The file 2d2r.pdb is exactly as I downloaded it from RCSB

**The first lines of the header:
HEADER    TRANSFERASE                             16-SEP-05   2D2R
TITLE     CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UNDECAPRENYL PYROPHOSPHATE
TITLE    2 SYNTHASE
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: UNDECAPRENYL PYROPHOSPHATE SYNTHASE;
COMPND   3 CHAIN: A, B;

**The opening ATOM records:
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.020149  0.000000  0.000000        0.00000
SCALE2      0.000000  0.016974  0.000000        0.00000
SCALE3      0.000000  0.000000  0.006518        0.00000
ATOM      1  N   SER A   3      -4.458  53.857  94.802  1.00 59.58           N
ATOM      2  CA  SER A   3      -4.745  52.989  93.628  1.00 59.67           C
ATOM      3  C   SER A   3      -3.414  52.652  92.952  1.00 59.42           C
ATOM      4  O   SER A   3      -2.843  51.569  93.142  1.00 59.53           O