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:
get-model.py
------
from modeller import *
from modeller.automodel import
*
env = environ()
env.io.atom_files_directory = './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
a.make()
------
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 "get-model.py", line 23, in ?
a.make()
File
"/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 108, in
make
self.homcsr(exit_stage)
File
"/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 419, in
homcsr
self.make_initial_model(aln)
File
"/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 433, in
make_initial_model
self.generate_method(self,
aln)
File
"/usr/lib/modeller9v1/modlib/modeller/automodel/generate.py", line 25, in
transfer_xyz
mdl.create_topology(aln)
File
"/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 605, in
create_topology
self.special_patches(aln)
File "get-model.py", line 13, in special_patches
self.patch(residue_type='ACE', residues='1:')
File
"/usr/lib/modeller9v1/modlib/modeller/model.py", 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