-------- Original Message -------- Subject: five ss bridges Date: Thu, 02 Aug 2007 10:58:11 -0400 From: Dany Naranjo Feliciano dany@censa.edu.cu To: modeller_usage-owner@salilab.org

-----Original Message----- From: "Dany Naranjo Feliciano" dany@censa.edu.cu To: modeller_usage@salilab.org 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