To Whom It May Concern:

I'm attempting to use modeller to use two templates to model on short sequence.  I'm also creating the alignment file (PIR format) on my own and I'm having some troubles with one of my sequences.  My alignment file is as follows:

>P1;15c8
structure:15c8:1:H:217:H::::
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQKPEQGLEWIAQI
DPANGNTKYDPKFQGKATITADTSSNTAYLHLSSLTSEDSAVYY-----CA
ADPPYYG--------------HGDYWGQGTTLTVSSAKTTPPSVYPLAPGS
AAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSS
SVTVPSSTWPSETVTCNVAHPASSTKVDKKIV-----*
>P1;1fns
structure:1fns:1:H:225:H::::
QVQLKESGPGLVAPSQSLSITCTVSGFSLTDYGVDWVRQPPGKGLEWLGMI
WGD-GSTDYNSALKSRLSITKDNSKSQVFLKMNSLQTDDTARYYCVRDP--
-------ADYGNYDYALDYWG------QGTSVTVSSAKTTPPSVYPLAPGS
AAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSS
SVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG*
>P1;1f11
sequence:1f11:1::15:::::
---------------------------------------------------
--------------------------------------------CANDY--
---GSTY--------GFAYWG------------------------------
---------------------------------------------------
-------------------------------------*

The script that was run (quite simple):

from modeller.automodel import *

log.verbose()
env = environ()
a = automodel(env, alnfile='modAln.ali',
              knowns=('15c8','1fns'), sequence='1f11')
a.starting_model = 1
a.ending_model = 5
a.make()

And then the log file with the error:

openf5__224_> Open       11  OLD  SEQUENTIAL  $(LIB)/restyp.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v1}/modlib/resdih.lib
rdrdih__263_> Number of dihedral angle types         :        9
              Maximal number of dihedral angle optima:        3
              Dihedral angle names                   :  Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v1}/modlib/radii.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v1}/modlib/radii14.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v1}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes:  APBLE
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v1}/modlib/mnch.lib
rdclass_257_> Number of classes:        5
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v1}/modlib/mnch1.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v1}/modlib/mnch2.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v1}/modlib/mnch3.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL8v1}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types:       21
runcmd______> alignment.append(align_codes=['15c8', '1fns', '1f11'], atom_files=[], file='modAln.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True)

openf___224_> Open           modAln.ali

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      2124923    2075.120     2.026

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      2126623    2076.780     2.028

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      2130023    2080.101     2.031

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      2136823    2086.741     2.038

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      2457301    2399.708     2.343

Read the alignment from file       : modAln.ali
Total number of alignment positions:   241

  #  Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
  1       15c8     217      1        15c8
  2       1fns     225      1 pdb1fns.ent
  3       1f11      15      1        1f11
runcmd______> alignment.check()

check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open       11  OLD  SEQUENTIAL  pdb15c8.ent

Dynamically allocated memory at   amaxstructure [B,kB,MB]:      2579199    2518.749     2.460
openf5__224_> Open       11  OLD  SEQUENTIAL  pdb15c8.ent
openf5__224_> Open       11  OLD  SEQUENTIAL  pdb1fns.ent
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:  1: H
rdabrk__288W> Protein not accepted:        2
check_a_337E> Structure not read in:        2

I'm running version 8v1 on Fedora core 3.  The best that I can decipher is that modeller can't understand the starting position.  Or perhaps it can't find the chain.  The pdb file has the same exact sequence (minus the gaps of course) and chain id H. 

Interestingly (or confusingly) I also tried replacing the residue start and end with the words 'FIRST' and 'LAST' leaving the chain
H, thinking that Modeller could grab the chain without me telling it where to start and end explicitly.  The end of the error file was as follows:

Total number of alignment positions:   241

  #  Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
  1       15c8     217      1        15c8
  2       1fns     225      1        1fns
  3       1f11      15      1        1f11
runcmd______> alignment.check()

check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open       11  OLD  SEQUENTIAL  pdb15c8.ent

Dynamically allocated memory at   amaxstructure [B,kB,MB]:      2579199    2518.749     2.460
openf5__224_> Open       11  OLD  SEQUENTIAL  pdb15c8.ent
openf5__224_> Open       11  OLD  SEQUENTIAL  pdb1fns.ent

Dynamically allocated memory at   amaxstructure [B,kB,MB]:      2703099    2639.745     2.578
openf5__224_> Open       11  OLD  SEQUENTIAL  pdb1fns.ent
rdabrk__290E> Number of residues in the alignment and  pdb files are different:
     225      220
              For alignment entry:        2
rdabrk__288W> Protein not accepted:        2
check_a_337E> Structure not read in:        2


Okay, so modeller thinks there are 220 residues in the pdb file? Is it looking at the right chain? The other chains in that file are length 217 and 195 (which isn't 220).  It's looking at the correct file, who knows what chain it's going for.  Anything I try here ends up giving me different results in the log file (like FIRST and 225, modeller tells me it found 11 residues in the pdb file). 

Perhaps I'm way off in my thinking and I have some huge error in my alignment file.  I've tried modelling with three proteins (in the very same way, just a different protein for this problem one) and I was getting very similar errors.  I can't make the second protein be able to be read in.  Any help would be appreciated.

Kevin