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:
***************************** # 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
*****************************
>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