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