Hi, When I use this script some parts of my protein appears streched. Should I put water molecule for better refinment? Why I obtein worse models with refine option?
#Modelación por homología con un ligando transferido desde el molde
from modeller import * # Carga las clases del Modeller from modeller.automodel import * # Carga la clase automodel
log.verbose() # Solicita una salida detallada env = environ() # Crea un nuevo ambiente para construir para construir el modelo
# Directorio del fichero pdb/atm de entrada env.io.atom_files_directory = './‘
# Lectura de los heteroátomos en el pdb molde env.io.hetatm = True a = dopehr_loopmodel(env, alnfile = 'hetatm2.ali', # Fichero del alineamiento knowns = '1gmyAok2.pdb', # Código del molde sequence = 'Q8I7B2_sequence') # Código del blanco a.starting_model= 1 # Índice del primer modelo a.ending_model= 50 # Índice del último modelo # (determina el número de modelos a calcular) a.md_level = refine.very_slow # refinar modelo
a.loop.starting_model = 1 a.loop.ending_model = 2 a.loop.md_level = refine.very_slow # refinar lazos a.make() # Hacer los modelo
Dany Naranjo Feliciano Lic. Bioquímica Grupo Biología Molecular Centro Nacional de Sanidad Agropecuaria (CENSA) Apartado 10. San José de las Lajas. La Habana. CP 32700. Cuba Teléfono 53-47-863014 ext 28
"Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu".
Dany Naranjo Feliciano wrote: > When I use this script some parts of my protein appears streched. > Should I put water molecule for better refinment? Why I obtein worse > models with refine option?
Poor models are usually a consequence of a poor alignment - they will only get worse with more refinement if your scoring function is bad, unless you simply have insufficient sampling. Refinement does not make your models worse otherwise, since it's using the same scoring function as any other optimization of the models.
In comparative modeling solvation is usually implicit, in that the solvation of the template is transfered to the target, so introduction of water molecules probably won't help you. If you have crystal waters, however, there may be some benefit in introducing them with appropriate distance restraints.
Ben Webb, Modeller Caretaker
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