Dear Modeller team,
I'm trying to get the format right for a multiple alignment, I did in HHpred server to use as input to modeller. I don't understand the error messages. I don't know if the errors are related to the PDB file since I have not changed anything in original PDB unless the extension. I would appreciate very much your advice.
Thanks in advance for your help! Maryam
***The input python script: # Comparative modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class
log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in
# directories for input atom files env.io.atom_files_directory = ['.', '../atom_files']
a = automodel(env, alnfile = 'XPF_nuc.ali', # alignment filename knowns = '1j23','4bxo', # codes of the templates sequence = 'XPF') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual comparative modeling
***The run command: mod9.11 model_test1.py
***atom_files: $ ls -l total 952 -rw-r--r-- 1 mfaridou users 121905 Aug 25 23:07 1j23.atm -rw-r--r-- 1 mfaridou users 121905 Aug 25 23:08 1j23.pdb -rw-r--r-- 1 mfaridou users 362313 Aug 25 23:08 4bxo.atm -rw-r--r-- 1 mfaridou users 362313 Aug 25 23:08 4bxo.pdb
*** input file XPF_nuc.ali >P1;1j23 structurex:1j23:5:A:125:A:HEFnuclease:Pyrococcus furiosus:1.78:0.248 QEGVKVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLFDQVKRLKEAYSRPIMIVEGS-LY---------GIRNVHPNAIRGAIAAVTVDF-GVPIIFSSTPEETAQYI*
>P1;4bxo structurex:4bxo:1:A:151:A:FANCMprotein:Homo sapiens:2.15:0.255 GSGSRPHLAGTHTSLRLPQEGKGTCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDREKTGD------TSRMFRRTKSYDSLLTTLIGA-GIRILFSSCQEETADLL*
>P1;XPF sequence:XPF:.:.:156:.::0.00: 0.00 RGTASADVSTDTRKAGGQEQNGTQQSIVVDMREFRSELPSLIHRRGIDIEPVTLEVGDYILTPEMCVERKSISDLIGSLNNGRLYSQCISMSRYYKRPVLLIEFDPSKPFSLTSRGALFQEISSNDISSKLTLLTLHFPRLRILWCPSPHATAELF*
***The runtime messages: 'import site' failed; use -v for traceback Traceback (most recent call last): File "model_test1.py", line 18, in ? a.make() # do the actual comparative modeling File "/home/software/software//modeller_v9.11/modlib/modeller/automodel/automodel.py", line 96, in make self.homcsr(exit_stage) File "/home/software/software//modeller_v9.11/modlib/modeller/automodel/automodel.py", line 423, in homcsr self.check_alignment(aln) File "/home/software/software//modeller_v9.11/modlib/modeller/automodel/automodel.py", line 405, in check_alignment aln.check() File "/home/software/software//modeller_v9.11/modlib/modeller/alignment.py", line 197, in check self.check_structure_structure(io=io) File "/home/software/software//modeller_v9.11/modlib/modeller/alignment.py", line 206, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb :