Hi there,
I am new to modeller and I have trouble creating a homology model of a protein using two templates. I modified the model-default.py script as shown below and I got error messages. I would appreciate it if any one can give me any suggestion.
Thanks. Thomas
Here is model-default.py script I am using: ##################################################################### # Homology modelling by the automodel class
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 = 'alignment1.ali', # alignment filename knowns = '2MDbis 1wu9', # codes of the templates sequence = 'flq15691') # 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 homology modelling
#########################################################################
my alignment file looks: ################################################################### >P1;2MDbis structureX:2MDbis:1 : :148 : :Eb1:Homo sapience: 1.90: 0.19 ..... >P1;1wu9 structureX:1wu9:A : :59 : :Eb1:Homo sapience: 1.90: 0.19 ...... >P1;flq15691 sequence:flq15691:1: :286::q15691:Homo sapience: 2.00: -1.00 ...... #####################################################################
I am getting the following error message ######################################################################## Traceback (most recent call last): File "model-default.py", line 18, in ? a.make() # do the actual homology modelling File "/usr/local/programs/modeller-8v2/modlib/modeller/automodel/automodel.py", line 100, in make self.homcsr(exit_stage) File "/usr/local/programs/modeller-8v2/modlib/modeller/automodel/automodel.py", line 318, in homcsr aln = self.read_alignment() File "/usr/local/programs/modeller-8v2/modlib/modeller/automodel/automodel.py", line 312, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/usr/local/programs/modeller-8v2/modlib/modeller/alignment.py", line 36, in append return self.__int_append('alignment.append', io, libs, vars) File "/usr/local/programs/modeller-8v2/modlib/modeller/alignment.py", line 68, in __int_append libs=libs.modpt, **vars) File "/usr/local/programs/modeller-8v2/modlib/modeller/util/top.py", line 33, in read_alignment return _modeller.read_alignment(aln, io, libs, *args) _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = flq15691 ###################################################################