Hi I try to model an heterodimer using this alignment
>P1;1DZB2 structureX:1DZB2:1:A:107:B:::: QVKLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCAR-----WDWYFDVWGQGTTVTVSSG/ ------------DIELTQSPSSMYTSLGERVTITCKASQDINSYLRWFQQKPGKSPKTLIYYATSLADGVPSRFSGSGSGQDYSLTISSLESDDTTTYYCLQHGESPYTFGGGTKLEIK---------*
>P1;atc sequence::::::::: -VKLQQSGGGLVQPGGSLKLSCAASGFDFSRYWMSWVRQAPGKGLEWIGEINPDSSTINYTPSLKDTFIISRDNAKNTLYLQMSKVRSEDTALYYCARQGYDGYHWYFDVWGQGTTVTVSSE/ SLDLGGGGGGGGDIQLTQSPSSLSASVGETVTLTCGASENIYGGLNWYQRKQGKSPQLLIYGATKLADGMSSRFSGGGSGRQYFLKITSLHPDDVATYYCQNVLSNPLTFGAGTKLELKRADAAPTVS*
each time it gives me this error message define__595E> Number of selected atoms in sets 2 & 3 is not the same: 121 128
Can you tell me please what's wrong in my alignment file
script used: # Homology modeling by the automodel class # # Demonstrates how to build multi-chain models, and symmetry restraints # from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) env = environ() # directories for input atom files env.io.atom_files_directory = './'
a = MyModel(env, alnfile = 'ali.pir', knowns = '1DZB2', sequence = 'atc') a.starting_model= 1 a.ending_model = 1
a.make()
On 4/4/11 5:06 PM, Houcemeddine Othman wrote: > I try to model an heterodimer using this alignment
If it's a heterodimer, why are you imposing symmetry restraints? The two subunits won't be the same.
> each time it gives me this error message > define__595E> Number of selected atoms in sets 2 & 3 is not the > same: 121 128
You can't make two differently-sized sets of atoms symmetric.
> Can you tell me please what's wrong in my alignment file
There's nothing wrong with your alignment file. But remove the symmetry restraint from your Python script (in this case, use the automodel class rather than MyModel).
Ben Webb, Modeller Caretaker
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Houcemeddine Othman -
Modeller Caretaker