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
On 10/30/15 12:03 PM, Qiang Zhong wrote: > 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?
As described in the manual, loopmodel does regular comparative modeling (which will perturb the whole structure, of course) and then loop refinement. If you only want the loop refinement, see http://salilab.org/modeller/9.15/manual/node36.html
Ben Webb, Modeller Caretaker
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Qiang Zhong