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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