Please help me ....where is the problem:error is :-------------------------- 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 "Sec-struct-restrain-copy.py", line 10 def special_restraints(self, aln): ^ IndentationError: expected an indented block ------------------------------here is the python script for model building:#model with restrainin sec. structure and optimization after modeling, by MD from modeller import * from modeller.automodel import * # Load the automodel class
# directories for input atom files
class MyModel (automodel): def special_restraints(self, aln):
# Residues should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range(’10:’, ’30:’))) rsr.add(secondary_structure.alpha(self.residue_range(’41:’, ’49:’))) rsr.add(secondary_structure.alpha(self.residue_range(’54:’, ’59:’))) rsr.add(secondary_structure.alpha(self.residue_range(’61:’, ’66:’))) rsr.add(secondary_structure.alpha(self.residue_range(’80:’, ’100:’))) rsr.add(secondary_structure.alpha(self.residue_range(’104:’, ’107:’))) rsr.add(secondary_structure.alpha(self.residue_range(’180:’, ’200:’))) rsr.add(secondary_structure.alpha(self.residue_range(’202:’, ’207:’))) rsr.add(secondary_structure.alpha(self.residue_range(’210:’, ’219:’))) # Residues should be beta-strands: rsr.add(secondary_structure.strand(self.residue_range(’111:’, ’116:’))) rsr.add(secondary_structure.strand(self.residue_range(’133:’, ’135:’))) rsr.add(secondary_structure.strand(self.residue_range(’144:’, ’146:’))) rsr.add(secondary_structure.strand(self.residue_range(’158:’, ’164:’)))
log.verbose() env = environ() env.io.atom_files_directory = ['.', './template_struc'] a = automodel (env,
alnfile = ’Q99720-3CIA_AA.ali’, # alignment filename knowns = ’3CIA_A’, # codes of the templates sequence = ’Q99720’) # code of the target a.starting_model= 1 # index of the first model a.ending_model = 10 # index of the last model
--------------------------------------------please help me out ......i am trying last few months for this .. I will be highly thankful to you. RegardsPKG
Dr. Pawan Kumar GuptaResearch Scientist CNS, Active Compound Library Latvian Institute of Organic SynthesisRiga, Latvia Office: +371-22374710 Website: https://sites.google.com/site/pawanpharma79/
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