Dear all

I try to add the terminal residues such as, ACE or CT3,to the N-Term or C-Term, but it always gave the error message, therefore, I come here for help. I used the modeller9,and  the "py" file I using for patch is as following:

from modeller  import *
from modeller.automodel import *

env = environ() = './atom_files'

env.patch_default = False
class mymodel(automodel):
    def special_patches(self, aln):
        # Acetylate the N terminus
       self.patch(residue_type='ACE', residues='1:')
        # Standard C terminal patch
       self.patch(residue_type='CT3', residues='238:')

# Disable default NTER and CTER patches

a = mymodel(env, alnfile='apde.ali',
            knowns=('1pqg', 'Hd2S', '1lo2'), sequence='apde')
a.starting_model = 1
a.ending_model = 1


The error message is as following:


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
Traceback (most recent call last):
  File "", line 23, in ?
  File "/usr/lib/modeller9v1/modlib/modeller/automodel/", line 108, in make
  File "/usr/lib/modeller9v1/modlib/modeller/automodel/", line 419, in homcsr
  File "/usr/lib/modeller9v1/modlib/modeller/automodel/", line 433, in make_initial_model
    self.generate_method(self, aln)
  File "/usr/lib/modeller9v1/modlib/modeller/automodel/", line 25, in transfer_xyz
  File "/usr/lib/modeller9v1/modlib/modeller/automodel/", line 605, in create_topology
  File "", line 13, in special_patches
    self.patch(residue_type='ACE', residues='1:')
  File "/usr/lib/modeller9v1/modlib/modeller/", line 155, in patch
    raise TypeError, "expecting one or more 'residue' objects"""
TypeError: expecting one or more 'residue' objects


please give some advice, thank you very much in advance.

Jin Ming


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