Hi:
My target protein is a member of GPCR.I used multiple template to build the model,
there was no overlap among the templates. The final model was not reasonable. The
C-tail and N-tail were away from transmember region, simultaneity,located flank of
transmember region.I want to know, was there any restraints on 'MODELLER'?
the following is alignment:
>P1;proteinA
structureX:proteinA
aaaaaaaaaaaaaaaaaaaaaaaaaaaa----------------------------------*
>P1;proteinB
structureX:proteinB
----------------------------bbbbbbbbbbbbbbbbbbbbbbbbb---------*
>P1;proteinC
structureX:proteinC
-----------------------------------------------------ccccccccc*
>P1;model
sequence:model
aaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbcccccccccc*
The following was my script:
from modeller import *
from modeller.automodel import *
env = environ()
a = automodel(env, alnfile='model_mult.ali',
knowns=('proteinA','proteinB', 'proteinC' ), sequence='model')
a.starting_model = 1
a.ending_model = 1
a.make()
was I missing something important? Or, did it in a wrong way?
looking for your reply!
thanks!
