[modeller_usage] help--model-segment.py

["" <>]

Hi:
  My target protein is GPCR, I use bovin rhodopsin as template.And, I alignment
the transmenbrane regions between template and target protein.I build model using
the fllowing scripts:
from modeller import *
from modeller.automodel import *
log.verbose()
class mymodel(automodel):
    def select_atoms(self):
        return selection(self.residue_range('37:A','63:A'),
                         self.residue_range('74:A','96:A'),
		         self.residue_range('111:A','133:A'),
		         self.residue_range('153:A','173:A'),
       		         self.residue_range('203:A','224:A'),
		         self.residue_range('250:A','274:A'),
		         self.residue_range('287:A','308:A'))
env=environ()
env.io.atoms_files_directory='./:../atom_files'
env.edat.nonbonded_sel_atoms=2

a=mymodel(env,
          alnfile='1u19-tm.ali',
	  knowns='1u19',
	  sequence='mrg-tm')
a.starting_model=1
a.ending_model=1
a.make()

But there are some errors:
Traceback (most recent call last):
  File "selection.py", line 23, in ?
    a.make()
  File "/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 118, in
make
    atmsel = self._check_select_atoms()
  File "/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 483, in
_check_select_atoms
    atmsel = self.select_atoms()
  File "selection.py", line 6, in select_atoms
    return selection(self.residue_range('37:A','63:A'),
  File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 64, in
residue_range
    start = self.residues[start]._num
  File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 165, in
__getitem__
    (self.offset, self.length, self.suffix))
  File "/usr/lib/modeller9v1/modlib/modeller/util/modutil.py", line 76, in
handle_seq_indx
    int_indx = lookup_func(*args)
  File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 50, in
_indxres
    raise KeyError, ("No such residue: %s" % indx)
KeyError: 'No such residue: 37:A'
How to repair the script?
The following is alignment file:
>P1;1u19
structureX:1u19:   1 :A:+348 :A:undefined:undefined:-1.00:-1.00
MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQ---
FSMLAAYMFLLIMLGFPINFLTLYVTV
QHKKLRTPLN
--YILLNLAVADLFMVFGGFTTTLY
TSLHGYFVFGPTGC--
NLEG--FFATLGGEIALWSLVVLAI
---ERYVVVCKPMSNFRFGENH
--AIMGVAFTWVMALACAAPPLV
GWSRYIPEGMQCSCGIDYYTPHEETNNES
FVIYMFVVHFIIPLI---VIFFCYG
QLVFTVKEAAAQQQESATTQKAEKE
VTRMVIIMVIAFLICWLPYAGVAFY
----IFTHQGSDFGPI-
FMTIPAFFAKTSAVYNPVIYIM-
-------MNKQFRNCMVTTLCCGKNP-LGDDEASTTVSKTETSQVAPA*
>P1;mrg-tm
sequence:mrg-tm:     : :     : ::: 0.00: 0.00
---------------------------------------
LS-LTVLTCIVSLVGLTGNAVVLWLLG
----------
FSIYILNLAAADFLFLSGRLIYSL-
----------------
ILYPVMMFSYFAG-LSFLSAV----
---------------------
HLSAVVCVLLWALSLLRS---IL
-----------------------------
FITVAWLIFLCVVLCGSSLVLLI--
-------------------------
-YVTILLTVLVFLLCGLPF-GIQFF
-----------------
LVSI--FLSALNSSANPIIYFFV
------------------------------------------------*

thank you very much!