Hello: I am running modeller job by "python model-parall.py" based on the following scrips. But it is said in the termial which seems that modeller coundn't find the template pdb file. However, my template pdb file is already in the same working directory which named pt6A.pdb. I don't why it said couldn't find it. Would you please give me some advices?
File "/soft/python2.5/lib/python2.5/site-packages/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/soft/python2.5/lib/python2.5/site-packages/modeller/automodel/automodel.py", line 411, in homcsr aln = self.read_alignment() File "/soft/python2.5/lib/python2.5/site-packages/modeller/automodel/automodel.py", line 401, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/soft/python2.5/lib/python2.5/site-packages/modeller/alignment.py", line 81, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = pt6
---------------------------------------------------------------------------------------- # Homology modeling by the automodel class, using multiple processors from modeller import * from modeller.automodel import * # Load the automodel class from modeller.parallel import *
# Use 2 CPUs in a parallel job on this machine j = job() j.append(local_slave()) j.append(local_slave())
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&
nbsp; = 'a8-pt6.ali', # alignment filename knowns = 'pt6', # codes of the templates sequence = 'a8') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.use_parallel_job(j) # Use the job for model building a.make() # do the actual homology modeling