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