I want to model missing loop in a protein, when I use loopmodel method do it, I got the perturbation of whole protein structure , my code is below, could you help me solve this problem?
a = loopmodel(env, alnfile = 'alignment.ali', # alignment filename knowns = '5fd1', # codes of the templates sequence = 'xxx') # 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 = 1 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level
a.make() # do homology modeling Qiang Zhong 010-64889893 Institute of Biophysics, Chinese Academy of Sciences E-mail:zhongqiang(AT)moon.ibp.ac.cn