Hi list, The models miss the 40 first aa of the sequence. What might be wrong? Thanks >P1;1gmy_A.pdb structureX:1gmy_A.pdb: 0 :A: 253 :A:undefined:undefined:-1.00:-1.00 KLPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDL LTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGSR-PP CTGEG-DTPKCSKICEPGYSPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVY SDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQ DHCGIESEVVAGIPRT* >P1;Q8I7B2_sequence --------------------IPDQSSCGSCWAVAGVGAMSDRVCIHSNGMMQPELSAIDL VSCC-SYCGNGCQGGSPPAAWDYWWRNGIVTGGTLENPTGCLPYPFPQCRHPGSRSQLNP CPRYTYPTPSCYPYCQAGYDKTYEKDKVYGKTSYNVDRHEYTIMEEIMKNGPVEAGFIVY TDFAVYKSGIYHHVSGRYAGKHAIRIIGWGVENGVKYWLTANSWNVGWGENGYFRILRGT DECRIESIVVAGMPR-*

# Homology modelling by the automodel class 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 = 'test_fasciola.ali', # alignment filename knowns = '1gmy_A.pdb', # codes of the templates sequence = 'Q8I7B2_sequence') # 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 modelling

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