Dear Modeller team,

I'm trying to get the format right for a multiple alignment, I did in HHpred server to use as input to modeller. I don't understand the error messages. I don't know if the errors are related to the PDB file since I have not changed anything in original PDB unless the extension. I would appreciate very much your advice.

Thanks in advance for your help!

Maryam

***The input python script:
# Comparative modeling by the automodel class
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 = ['.', '../atom_files']

a = automodel(env,
              alnfile = 'XPF_nuc.ali',     # alignment filename
              knowns   = '1j23','4bxo',     # codes of the templates
              sequence = 'XPF')              # code of the target
a.starting_model= 1                 # index of the first model
a.ending_model = 1                 # index of the last model
                                    # (determines how many models to calculate)
a.make()                            # do the actual comparative modeling

***The run command:
mod9.11 model_test1.py

***atom_files:
$ ls -l
total 952
-rw-r--r-- 1 mfaridou users 121905 Aug 25 23:07 1j23.atm
-rw-r--r-- 1 mfaridou users 121905 Aug 25 23:08 1j23.pdb
-rw-r--r-- 1 mfaridou users 362313 Aug 25 23:08 4bxo.atm
-rw-r--r-- 1 mfaridou users 362313 Aug 25 23:08 4bxo.pdb

*** input file XPF_nuc.ali
>P1;1j23
structurex:1j23:5:A:125:A:HEFnuclease:Pyrococcus furiosus:1.78:0.248
QEGVKVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLFDQVKRLKEAYSRPIMIVEGS-LY---------GIRNVHPNAIRGAIAAVTVDF-GVPIIFSSTPEETAQYI*

>P1;4bxo
structurex:4bxo:1:A:151:A:FANCMprotein:Homo sapiens:2.15:0.255
GSGSRPHLAGTHTSLRLPQEGKGTCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDREKTGD------TSRMFRRTKSYDSLLTTLIGA-GIRILFSSCQEETADLL*

>P1;XPF
sequence:XPF:.:.:156:.::0.00: 0.00
RGTASADVSTDTRKAGGQEQNGTQQSIVVDMREFRSELPSLIHRRGIDIEPVTLEVGDYILTPEMCVERKSISDLIGSLNNGRLYSQCISMSRYYKRPVLLIEFDPSKPFSLTSRGALFQEISSNDISSKLTLLTLHFPRLRILWCPSPHATAELF*

***The runtime messages:
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "model_test1.py", line 18, in ?
    a.make()                            # do the actual comparative modeling
File "/home/software/software//modeller_v9.11/modlib/modeller/automodel/automodel.py", line 96, in make
    self.homcsr(exit_stage)
File "/home/software/software//modeller_v9.11/modlib/modeller/automodel/automodel.py", line 423, in homcsr
    self.check_alignment(aln)
File "/home/software/software//modeller_v9.11/modlib/modeller/automodel/automodel.py", line 405, in check_alignment
    aln.check()
File "/home/software/software//modeller_v9.11/modlib/modeller/alignment.py", line 197, in check
    self.check_structure_structure(io=io)
File "/home/software/software//modeller_v9.11/modlib/modeller/alignment.py", line 206, in check_structure_structure
    return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb :