joelsubach@Joels-MacBook-Air 7dwbOPM_Monomer_LP % /usr/bin/python3
Python 3.8.9 (default, Apr 13 2022, 08:48:06)
[Clang 13.1.6 (clang-1316.0.21.2.5)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from modeller import *
>>> from modeller.automodel import *    # Load the AutoModel class
>>>
>>> log.verbose()
>>> env = Environ()

                         MODELLER 10.3, 2022/07/08, r12388

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                     Copyright(c) 1989-2022 Andrej Sali
                            All Rights Reserved

                             Written by A. Sali
                               with help from
              B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
          M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
             A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
                     F. Melo, J.P. Overington, E. Feyfant
                 University of California, San Francisco, USA
                    Rockefeller University, New York, USA
                      Harvard University, Cambridge, USA
                   Imperial Cancer Research Fund, London, UK
              Birkbeck College, University of London, London, UK


Kind, OS, HostName, Kernel, Processor: 4, Darwin Joels-MacBook-Air.local 21.6.0 arm64
Date and time of compilation         : 2022/07/08 12:37:28
MODELLER executable type             : mac11arm64-gnu
Job starting time (YY/MM/DD HH:MM:SS): 2022/09/02 16:50:46

openf___224_> Open           $(LIB)/restyp.lib
openf___224_> Open           ${MODINSTALL10v3}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups:        2
openf___224_> Open           ${MODINSTALL10v3}/modlib/sstruc.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       191566     187.076     0.183

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       192094     187.592     0.183
openf___224_> Open           ${MODINSTALL10v3}/modlib/resdih.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       240694     235.053     0.230
rdrdih__263_> Number of dihedral angle types         :        9
              Maximal number of dihedral angle optima:        3
              Dihedral angle names                   :  Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open           ${MODINSTALL10v3}/modlib/radii.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       253994     248.041     0.242
openf___224_> Open           ${MODINSTALL10v3}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes:  APBLE
openf___224_> Open           ${MODINSTALL10v3}/modlib/mnch.lib
rdclass_257_> Number of classes:        5
openf___224_> Open           ${MODINSTALL10v3}/modlib/mnch1.lib
openf___224_> Open           ${MODINSTALL10v3}/modlib/mnch2.lib
openf___224_> Open           ${MODINSTALL10v3}/modlib/mnch3.lib
openf___224_> Open           ${MODINSTALL10v3}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types:       21
>>>
>>> # directories for input atom files
>>> env.io.atom_files_directory = ['.', '../atom_files']
>>>
>>> class MyModel(AutoModel):
...     def select_atoms(self):
...         return Selection(self.residue_range('88:A', '99:A')
...
... a = MyModel(env, alnfile = 'alignment.ali',
  File "<stdin>", line 5
    a = MyModel(env, alnfile = 'alignment.ali',
    ^
SyntaxError: invalid syntax
>>>               knowns = '7dwbOPM_chainA', sequence = '7dwbOPM_chainA_fill')
  File "<stdin>", line 1
    knowns = '7dwbOPM_chainA', sequence = '7dwbOPM_chainA_fill')
    ^
IndentationError: unexpected indent
>>> a.starting_model = 1
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
NameError: name 'a' is not defined
>>> a.ending_model   = 1
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
NameError: name 'a' is not defined
>>>
>>> a.make()

TEXT FILE BELOW:

from modeller import *
from modeller.automodel import *    # Load the AutoModel class

log.verbose()
env = Environ()

# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']

class MyModel(AutoModel):
    def select_atoms(self):
        return Selection(self.residue_range('88:A', '99:A')

a = MyModel(env, alnfile = 'alignment.ali',
              knowns = '7dwbOPM_chainA', sequence = '7dwbOPM_chainA_fill')
a.starting_model = 1
a.ending_model   = 1

a.make()