Recently, I installed Modeller 10.4 software into my windows 10, 10GB RAM, 64x bit laptop to predict a 3D structure of a membrane protein (a.a length 574).
In this case , i used advanced modeller option to prediction. Because we can use multiple templates for structure prediction. But from the start I got errors when running the python script.
1)May I know what is the maximum number of templates,which can be used for advanced modeling.
Hi! I have previously done protein modeling with different chains and different tempering. I have never read that Modeller has a limit of tempalds to use, there may be a bug in your code.
Here I send (for modeling part) you an example that I have previously used to generate monomers.
from modeller import *
from modeller.automodel import *
#from modeller import soap_protein_od
log.verbose() # request verbose output
env = Environ()
a = automodel(env, alnfile='aligment.ali',
knowns=("template_1","template_2"), sequence='target',
assess_methods=(assess.DOPE,
#soap_protein_od.Scorer(),
assess.GA341))
a.starting_model = 1
a.ending_model = 100
a.make()
I hope you find it useful!
Here you can see better the format. If you want you can send me your code to check it.
- Badges
- Science topic