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 templatesfrom modeller import * # Load standard Modeller classesfrom modeller.automodel import * # Load the automodel classlog.verbose() # request verbose outputenv = environ() # create a new MODELLER environment to build this model in# directories for input atom filesenv.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 targeta.starting_model= 1 # index of the first modela.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_filestotal 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;2d2rstructureX:2d2r:A:3:A:227:UPP :Helicobacter pylori: :---------------------------------------MLSATQPLSEKLDST-LKHLAIIMDGNGRWAKLKNK-ARAYGHKKGVKTLKDITIWCANHKLECLTLYAFSTENWKRPKSEVDFLMKMLKKYLK---DERSTYLDNNIRFRAIGDLEGFSKELRDTILQLENDTRHFKDFTQVLALNYGSKNELSRAFKSLLESPPS-NISLLE---------------------SLENEISNRLDTRNLPEVDLLLRTGGEMRLSNFLLWQSSYAELFFTPILWPDFTPKDLENIISDFYKRVRKFGELKA-----*>P1;1uehstructureX:1ueh:A:13:A:240 :UPP :Erischeria coli : : --------------------------------------MMLSATQPLSEKLPAHGCRHVAIIMDGNGRWAKKQGK-IRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALD---SEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQ---------------------IDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRERRFGGTEPGDETA*>P1;2vg3structureX:2vg3:A:13:A:296:rv2361c decaprenyl PP:M. tuberculosis: : FPQLPPAPDDYPTFPDTSTWPVVFPELPAAPYGGPCRPPQHTSKAAAPRIPADRLPNHVAIVMDGNGRWATQRGL-ARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFSTENWKRSPEEVRFLMGFNRDVVR---RRRDTLKKLGVRIRWVGSRPRLWRSVINELAVAEEMTKSNDVITINYCVNYGGRTEITEATREIAREVAAGRLNPER---------------------ITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYAEYIFQDKLWPDYDRRDLWAACEEYASRTRRFGSA-------*>P1;1f75structureX:1f75:A:14:A:242:UPP :Micrococcus luteus: :-----------------------------------MFPIKKRKAIKNNNINAAQIPKHIAIIMDGNGRWAKQKKM-PRIKGHYEGMQTVRKITRYASDLGVKYLTLYAFSTENWSRPKDEVNYLMKLPGDFLN---TFLPELIEKNVKVETIGFIDDLPDHTKKAVLEAKEKTKHNTGLTLVFALNYGGRKEIISAVQLIAERYKSGEISLDE---------------------ISETHFNEYLFTANMPDPELLIRTSGEERLSNFLIWQCSYSEFVFIDEFWPDFNEESLAQCISIYQ---------------*>P1;2vg0structureX:2vg0:A:30:A:256:Rv 1086 farnesyl PP:M. tuberculosis: : -----------------------------------------------------DLPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVE---EICAPANHWSVRT--VGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDA-----------------VTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSAR--------------*>P1;2cptsequence:2cpt::1: :316:rubber c-prenylxferase:Hevea brasiliensis: :-----------------------MELYTGERPSVFRLLGKYMRKGLYGILTQGPIPTHLAFILDGNRRFAKKHKL-PEGGGHKAGFLALLNVLTYCYELGVKYATIYAFSIDNFRRKPHEVQYVMDLMLEKIEGMIMEESIINAYDICVRFVGNLKLLSEPVKTAADKIMRATANNSKCVLLIAVCYTSTDEIVHAVEESSELNSNEVCNNQELEEANATGSSTVIQTENMESYSGIKLVDLEKNTYINPYPDVLIRTSGETRLSNYLLWQTTNCILYSPHALWPEIGLRHVVWAVINCQRHYSYLEKHKEYLK--****The runtime messages:[newhoir@localhost rubber]$ ./r'import site' failed; use -v for tracebackTraceback (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", line424, in homcsr self.check_alignment(aln) File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line406, 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, incheck_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)_modeller.ModellerError: rdpdb___303E> No atoms were read from the specifiedinput PDB file, since the starting residue number and/or chain id inMODEL_SEGMENT (or the alignment file header) was not found; requested startingposition: 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 2D2RTITLE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UNDECAPRENYL PYROPHOSPHATETITLE 2 SYNTHASECOMPND 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 0.00000ORIGX3 0.000000 0.000000 1.000000 0.00000SCALE1 0.020149 0.000000 0.000000 0.00000SCALE2 0.000000 0.016974 0.000000 0.00000SCALE3 0.000000 0.000000 0.006518 0.00000ATOM 1 N SER A 3 -4.458 53.857 94.802 1.00 59.58 NATOM 2 CA SER A 3 -4.745 52.989 93.628 1.00 59.67 CATOM 3 C SER A 3 -3.414 52.652 92.952 1.00 59.42 CATOM 4 O SER A 3 -2.843 51.569 93.142 1.00 59.53 O