Dear Modeller-Usage group,

I have a problem with my structure. It is lacking 9 amino acids from a loop next to its active center. I've tried to refill it using the loopmodel class script from this tutorial: http://salilab.org/modeller/wiki/Missing%20residues. My script looks like this:

# Ab-initio modeling by the loopmodel 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 = 'sEH_AN_A.ali',
              knowns = 'sEH_AN_A', sequence = 'sEH_AN_A_fill',
              assess_methods=(assess.DOPE,
                              assess.GA341),
              loop_assess_methods=(assess.DOPE,
                              assess.normalized_dope,
                              assess.GA341))
a.starting_model= 1
a.ending_model  = 10

a.loop.starting_model = 1
a.loop.ending_model   = 10
a.loop.md_level       = refine.fast

a.make()

I've also find a homologous structure with a complete amino acid sequence but its sequence has only 34% identity with my structure. So I just cut the loop from the homologous and use it as a template. I think that the loop from my structure will be similar to the loop from the homologous structure. My second script looks like that

# 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 = automodel(env,
    alnfile  = 'sEH_AN-homolog.ali',    
    knowns   = ('homologue', 'sEH_AN_A'),             
    sequence = 'sEH_AN_A_fill',           
    assess_methods=(assess.DOPE,
                              assess.normalized_dope,
                              assess.GA341))
 
a.starting_model= 1                
a.ending_model  = 100            
 
a.make()                         

Then I compared all the models I've build by Z-score (normalized.DOPE) value and by calculating the RMSD of the created models and homologous structure. The RMSD is very high (1,55 to even 5,48) so I think the models are not so good.

Which method will give me more accurate and native-like models?

Best regards,
Karolina Markowska
Silesian University of Technology