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!