[modeller_usage] question about basic modelling

[Mehmet Serkan Apaydin <>]

Hi,

  I am a new MODELLER user. I am trying to duplicate a result in 
literature using v8.1 of MODELLER, and am trying to use 1H8C.pdb as 
template to model 1D3Z.pdb structure. I followed the basic outline of the 
scripts in the tutorial (and attached the scripts I used). At the end of 
modelling, the homology model I obtain is about 9A cRMSD from the target 
structure, whereas in the literature an earlier version of MODELLER (v6.2) 
was used to achieve a closer structure to the template (1.9A cRMSD). I was 
wondering whether there is any simple step I may be missing.

Thanks,

--Serkan

# Homology modelling by the automodel class

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  = '1D3Z-1H8C.ali',     # alignment filename
              knowns   = '1H8C',              # codes of the templates
              sequence = '1D3Z')              # 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)
# Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6
a.repeat_optimization = 3
a.max_molpdf = 1e6

a.loop.starting_model = 1           # First loop model
a.loop.ending_model   = 4           # Last loop model
a.loop.md_level       = refine.very_slow # Loop model refinement level

a.make()                            # do homology modelling

from modeller.automodel import *

log.verbose()
env = environ()
a = automodel(env, alnfile='1D3Z-1H8C.ali',
              knowns='1H8C', sequence='1D3Z')

# Very thorough VTFM optimization:
a.library_schedule = 1
a.max_var_iterations = 300

# Very thorough MD optimization:
#a.md_level = refine.very_slow

# Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6
#a.repeat_optimization = 3
#a.max_molpdf = 1e6

a.starting_model = 1
a.ending_model = 1
a.make()


env = environ()
aln = alignment(env)
mdl = model(env, file='1H8C')
aln.append_model(mdl, align_codes='1H8C', atom_files='1H8C.pdb')
aln.append(file='1D3Z.seq', align_codes='1D3Z')
aln.align2d()
aln.write(file='1D3Z-1H8C.ali', alignment_format='PIR')
aln.write(file='1D3Z-1H8C.pap', alignment_format='PAP')