Hi,
I try to do homology modeling by the automodel class. I get this error:
File "/usr/lib/modeller9.12/modlib/modeller/modeller/restraints.py", line 170, in make_distance
raise TypeError("restraint_group should be a physical_type object")
I used mod9.12 on Ubuntu 12.04 with python2.7, with those script and alignment file:
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# 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 = ['.', '../atom_files']
a = automodel(env,
alnfile = '1FLZ-WT-MU.ali', # alignment filename
knowns = '1FLZ', # codes of the templates
sequence = '1FLZ-H15Y-H206R') # 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
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>P1;1FLZ
structureX:1FLZ: 5 :A:229 :A:undefined:undefined:-1.00:-1.00
LTWHDVLAEEKQQPHFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIA
IPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLW
GSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQHGETPIDWMPVLPAESE*
>P1;1FLZ-H15Y-H206R
sequence:1FLZ-H15Y-H206R: : : : ::: 0.00: 0.00
LTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIA
IPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLW
GSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAESE*
*****************************
Where could this error come from?
Thanks a lot in advance,
Isaure