[modeller_usage] No atoms were read from the specified input PDB file

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.