Hi,

I am new to both Modeller and homology modeling, and trying to do a simple modeling with the following script but I keep getting the error:
Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(       1) = proe

# Homology 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 = ['.', '.']

a = automodel(env,
              alnfile = 'alignment6.ali',     # alignment filename
              knowns   = 'proe',              # codes of the templates
              sequence = 'alp7')              # 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 homology modeling

Here is my alignment6.ali file:

>P1; PROE
structureX:PROE:1:E:476:E:::-1.00:-1.00
-----------------------NEEGRLIEKLLGDYDKRIKPAKTLDHVIDVTLKLTLT
NLISLNEKEEALTTNVWIEIQWNDYRLSWNTSEYEGIDLVRIPSELLWLPDVVLENNVDG
QFEVAYYANVLVYNDGSMYWLPPAIYRSTCPIAVTYFPFDWQNCSLVFRSQTYNAHEVNL
QLSAEEGIDPEDFTENGEWTIRHRPAKKNYNWQLTKDDIDFQEIIFFLIIQRKPLFYIIN
IIAPCVLISSLVVLVYFLPAQAGGQKCTLSISVLLAQTIFLFLIAQKVPETSLNVPLIGK
YLIFVMFVSLVIVTNCVIVLNVSLRTPN--------------------------------
------------------------------------------------------------
-----------------THSCVEACNFIAKSTKEQNDSGSENENWVLIGKVIDKACFWIA
LLLFSLGTLAIFLTG--HLNQVPE---*

>P1; ALP7
sequence:ALP7:::::::0.00:0.00
MRCSPGGVWLALAASLLHVSLQGEFQRKLYKELVKNYNPLERPVANDSQPLTVYFSLSLL
QIMDVDEKNQVLTTNIWLQMSWTDHYLQWNVSEYPGVKTVRFPDGQIWKPDILLYNSADE
RFDATFHTNVLVNSSGHCQYLPPGIFKSSCYIDVRWFPFDVQHCKLKFGSWSYGGWSLDL
QMQEAD---ISGYIPNGEWDLVGIPGKRSERFYECCKEP-YPDVTFTVTMRRRTLYYGLN
LLIPCVLISALALLVFLLPADSG-EKISLGITVLLSLTVFMLLVAEIMPATSDSVPLIAQ
YFASTMIIVGLSVVVTVIVLQYHHHDPDGGKMPKWTRVILLNWCAWFLRMKRPGEDKVRP
ACQHKQRRCSLASVEMSAVAPPPASNGNLLYIGFRGLDGVHCVPTPDSGVVCGRMACSPT
HDEHLLHGGQPPEGDPDLAKILEEVRYIANRFRCQDESEAVCSEWKFAACVVDRLCLMAF
SVFTIICTIGILMSAPNFVEAVSKDFA*

Thanks,
tkucuk