Hi,
I am using the following code for a tetramer modelling:
from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() class MyModel(automodel): def special_restraints(self, aln): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, s3, s4)) def user_after_single_model(self): self.restraints.symmetry.report(1.0)
env = environ() env.io.atom_files_directory = ['.', '../atom_files']
a = MyModel(env, alnfile = 'qseq1-tseq1.ali' , # my alignment filename knowns = 'tseq1', # code of the tetramer template sequence = 'qseq1') # code of the monomer made with modeller
a.starting_model= 1 a.ending_model = 1
a.make()
but after running it, the console is showing "raise KeyError <"No such chain: %s" % indx> KeyError: 'No such chain: A'"
Please help me.
Regards,
Arijit Ghosh
On 2/24/15 5:56 AM, Arijit Ghosh wrote: > I am using the following code for a tetramer modelling: ... > but after running it, the console is showing "raise KeyError <"No such > chain: %s" % indx> > KeyError: 'No such chain: A'"
Your sequence in your alignment file is only a single chain (not four). You seem to be missing chain breaks (/ characters).
Ben Webb, Modeller Caretaker
You mean to say my target sequence has only one chain? Yes, but how can I make 4 chains with that sequence? My template sequence has 4 chains though, and it is separated by chain breaks.
Sent from my BlackBerry 10 smartphone. Original Message From: Modeller Caretaker Sent: Wednesday 25 February 2015 1:47 AM To: Arijit Ghosh; modeller_usage@salilab.org Subject: Re: [modeller_usage] Problem with tetramer modelling
On 2/24/15 5:56 AM, Arijit Ghosh wrote: > I am using the following code for a tetramer modelling: ... > but after running it, the console is showing "raise KeyError <"No such > chain: %s" % indx> > KeyError: 'No such chain: A'"
Your sequence in your alignment file is only a single chain (not four). You seem to be missing chain breaks (/ characters).
Ben Webb, Modeller Caretaker
On 2/24/15 6:09 PM, Arijit Ghosh wrote: > You mean to say my target sequence has only one chain? Yes, but how > can I make 4 chains with that sequence?
Modeller models what you give it. So if you want 4 chains in your model, your target sequence needs to have 4 chains too - the number of chains in the template is irrelevant. What you align the target with is up to you.
Ben Webb, Modeller Caretaker
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Arijit Ghosh -
Modeller Caretaker