[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[modeller_usage] [Fwd: five ss bridges]





-------- Original Message --------
Subject: 	five ss bridges
Date: 	Thu, 02 Aug 2007 10:58:11 -0400
From: 	Dany Naranjo Feliciano <>
To: 	







    -----Original Message-----
    From: "Dany Naranjo Feliciano" <>
    To: 
    Date: Thu, 02 Aug 2007 10:30:42 -0400
    Subject: five ss bridges

    Hi,
    I´m trying to model 5 SS bridges.
    When I try to tell modeller 9v1 to do that,I receive the following
    error:
    Could not find platform independent libraries <prefix>
    Could not find platform dependent libraries <exec_prefix>
    Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
    'import site' failed; use -v for traceback
    File "test_ssmodel_fasciola.py", line 9
    def special_patches(self, aln):
    ^
    IndentationError: expected an indented block

    What might be wrong?
    The script,
    #Homology modelling by the automodel class
    from modeller import * # Load standar Modeller classes
    from modeller.automodel import * # Load the automodel class
    #Redefine the special_patches routine to include the additional
    disulfides
    #(this routine)
    class mymodel(automodel):
    def special_patches(self, aln):
    # A disulfide between residues 10-51,44-47,43-110,80-114,88-100:
    self.patch(residue_type='DISU', residues=(self.residues['10'],
    self.residues['51']))
    self.patch(residue_type='DISU', residues=(self.residues['44'],
    self.residues['47']))
    self.patch(residue_type='DISU', residues=(self.residues['43'],
    self.residues['110']))
    self.patch(residue_type='DISU', residues=(self.residues['80'],
    self.residues['114']))
    self.patch(residue_type='DISU', residues=(self.residues['88'],
    self.residues['100']))
    log.verbose() # request verbose output
    env = environ() # create a new MODELLER environment to build this
    model in
    # directories for input atom files
    env.io.atom_files_directory = './'
    a = mymodel(env,
    alnfile = 'test_fasciola.ali', # alignment filename
    knowns = '1gmy_A.pdb', # codes of the templates
    sequence = 'Q8I7B2_sequence') # 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.make() # do the actual homology modelling


    Dany Naranjo Feliciano
    Lic. Bioquímica
    Grupo Biología Molecular
    Centro Nacional de Sanidad Agropecuaria (CENSA)
    Apartado 10. San José de las Lajas.
    La Habana. CP 32700. Cuba
    Teléfono 53-47-863014 ext 28



"Participe en Universidad 2008 del 11 al 15 de febrero del 2008.
Palacio de Convenciones. La Habana. Cuba.
http: //www.universidad2008.cu".


	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage