Build missing residues for multisubunit protein
Hi,
Do you have suggestions on how to build missing residues for a multisubunit protein while restricting non-missing residues from moving?
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from modeller import *from modeller.automodel import * # Load the automodel classlog.verbose()env = environ()# directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files']
class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('1', '1'), self.residue_range('1', '2'), self.residue_range('181','181'))
a = MyModel(env, alnfile = 'alignment.ali', knowns = 'nqo2', sequence = 'nqo2_fill')a.starting_model= 1a.ending_model = 1a.make()
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Thank you,
Kelly
On 07/29/2013 11:42 AM, Kelly Tran wrote: > Do you have suggestions on how to build missing residues for a > multisubunit protein while restricting non-missing residues from moving?
Sure, it's the same as for a single chain protein - the only difference is that you'd need to qualify each residue number with the chain it's in (e.g. residue_range('1:A', '1:A')). What problems did you run into?
Ben Webb, Modeller Caretaker
Hi Ben,
The error I receive is:
--- File "/Library/modeller-9.10/modlib/modeller/coordinates.py", line 298, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 1:B' ---
I separate the chains with '/' in my alignment file.
Thank you,
Kelly
On Mon, Jul 29, 2013 at 2:48 PM, Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 07/29/2013 11:42 AM, Kelly Tran wrote: > >> Do you have suggestions on how to build missing residues for a >> multisubunit protein while restricting non-missing residues from moving? >> > > Sure, it's the same as for a single chain protein - the only difference is > that you'd need to qualify each residue number with the chain it's in (e.g. > residue_range('1:A', '1:A')). What problems did you run into? > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/**modeller/http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/**listinfo/modeller_usagehttps://salilab.org/mailman/listinfo/modeller_usage >
On 07/29/2013 12:02 PM, Kelly Tran wrote: > The error I receive is: > > --- > File "/Library/modeller-9.10/modlib/modeller/coordinates.py", line > 298, in _indxres > raise KeyError("No such residue: %s" % indx) > KeyError: 'No such residue: 1:B' > --- > > I separate the chains with '/' in my alignment file.
See http://salilab.org/modeller/9.12/manual/node29.html
Modeller numbers residues in the entire protein starting at 1 by default; it doesn't reset the numbering to 1 when it starts a new chain.
Ben Webb, Modeller Caretaker
Thank you Ben.
Kelly
On Mon, Jul 29, 2013 at 3:05 PM, Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 07/29/2013 12:02 PM, Kelly Tran wrote: > >> The error I receive is: >> >> --- >> File "/Library/modeller-9.10/**modlib/modeller/coordinates.**py", line >> 298, in _indxres >> raise KeyError("No such residue: %s" % indx) >> KeyError: 'No such residue: 1:B' >> --- >> >> I separate the chains with '/' in my alignment file. >> > > See http://salilab.org/modeller/9.**12/manual/node29.htmlhttp://salilab.org/modeller/9.12/manual/node29.html > > Modeller numbers residues in the entire protein starting at 1 by default; > it doesn't reset the numbering to 1 when it starts a new chain. > > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/**modeller/http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/**listinfo/modeller_usagehttps://salilab.org/mailman/listinfo/modeller_usage >
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Kelly Tran -
Modeller Caretaker