Hi,
It is Python syntax error. I guess you have lost a "," after line :
knowns = '1j8fAA','1j8fBB','1j8fCC','1q1aA','1yc5A','2od7A'
moreover if you specify more then one element as an argument you should
probably wrap them into a list or tuple. Lets try this line:
knowns = ('1j8fAA','1j8fBB','1j8fCC','1q1aA','1yc5A','2od7A'),
hope that helps!
regards,
marcin
Tuesday 18 of December 2007 10:23:32 Urszula Uciechowska napisał(a):
> Dear Modeller users,
>
> I am trying to use the model-loop.py script:
>
> Homology modeling by the automodel class
> from modeller import *
> from modeller.automodel import * # Load the automodel class
>
> log.verbose()
> env = environ()
>
> # directories for input atom files
> env.io.atom_files_directory = './:../atom_files'
>
> a = loopmodel(env,
> alnfile = 'Sirt1-multi.ali',
> # alignment filename
> knowns = '1j8fAA','1j8fBB','1j8fCC','1q1aA','1yc5A','2od7A'
> # codes of the templates
> sequence = 'Sirt1' )
> # 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.md_level = None # No refinement of model
>
> a.loop.starting_model = 1 # First loop model
> a.loop.ending_model = 4 # Last loop model
> a.loop.md_level = refine.fast # Loop model refinement level
>
> a.make() # do homology modeling
>
> but i am getting the error
>
> 'import site' failed; use -v for traceback
> File "model-loop.py", line 14
> sequence = 'Sirt1' ) # code
> of the target ^
> SyntaxError: invalid syntax
>
> Could someone tell me how to figure out this error?
>
> thank you in advance
>
>
>
> Best Regards,
> Urszula Uciechowska
>
> MSc.PhD Student
> Medicinal Chemistry Group
> University of Halle-Wittenberg
> _______________________________________________
> modeller_usage mailing list
>
> https://salilab.org/mailman/listinfo/modeller_usage
>
> :.
--
Marcin Feder, Sr.Research Assistant, (+48-22) 597-07-45,
marcin(a-t)genesilico(d-o-t)pl
Laboratory of Bioinformatics and Protein Engineering | www.genesilico.pl
International Institute of Molecular and Cell Biology | www.iimcb.gov.pl
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