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I want to model ONLY magnesium ion (from protein B) on an already crystallized structure (protein A). So the sequence of my target and template is exactly the same. My alignment file is ---------------------------------------------------------------------------------------------------------------------------- >P1;proteinA structureX:proteinA: 37 :B:+266 :B:::-1.00:-1.00 -QYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGEGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH*
>P1;proteinB structureX:proteinB: 401 :A:+1 :A:::-1.00:-1.00 $--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*
>P1;target sequence:target: : : : ::: 0.00: 0.00 $QYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGEGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH*
when i run this script
from modeller import * from modeller.automodel import *
log.verbose() env = environ()
env.io.atom_files_directory = ['.', '../atom_files'] env.io.hetatm = True
a = automodel(env, alnfile = 'alignment.ali', knowns=('proteinA','proteinB'), sequence='target') a.starting_model= 1 a.ending_model = 1
a.make()
I am getting segmentation fault. Could you please help me? Regards Renu
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