Dear Modeller users
I generated the dimer by Modeller. Fasta sequence number of model(400) is 70 less than Fasta sequence number of template(470). Sequence identity between template and model is 24%.
after selecting the template, I aligned them, and then I did loop modeling. (I attached the code at the bottom.) Finally I got final pdb structure, but when I checked my model, I found the below warning message.
"Unusual bond length, unusual bond angle, Chirality deviations "
I am a beginner, so I don't what should I do to correct above warning message. Please help me, Any suggestions or comments are welcomed. Thanks.
Hyun.
---align2d.py---- from modeller import *
env = environ() aln = alignment(env) mdl = model(env, file='****', model_segment=('FIRST:A','LAST:B')) aln.append_model(mdl, align_codes='******', atom_files='*****') aln.append(file='******.ali', align_codes='*****') aln.align2d() aln.write(file='**************.ali', alignment_format='PIR') aln.write(file='**************.pap', alignment_format='PAP')
---model-loop.py----- # Homology modeling by the automodel class from modeller import * from modeller.automodel import * # Load the automodel class
log.verbose() env = environ()
# directories for input atom files env.io.atom_files_directory = ['.', '../atom_files']
a = loopmodel(env, alnfile = '***************.ali', # alignment filename knowns = '*******', # codes of the templates sequence = '******') # 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.md_level = None # No refinement of model
a.loop.starting_model = 1 # First loop model a.loop.ending_model = 50 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level
a.make() # do homology modeling