automodel vs loopmodel
When I run the automodel or the loopmodel classes, either way I get a target.B99990001.pdb for the structure of the final model. From the documentation, I understand that in the case of the loopmodel, an extra pdb file will be produced with refined loops. My question is: Should the models in files target.B99990001.pdb be the same whether I use automodel or loopmodel? (provided I'm using the same optimizations and all, I'm just changing the class name in the python script)
Thanks!
Mauricio Carrillo Tripp wrote: > When I run the automodel or the loopmodel classes, either way I get a > target.B99990001.pdb for the > structure of the final model. From the documentation, I understand that > in the case of the loopmodel, an > extra pdb file will be produced with refined loops. > My question is: > Should the models in files target.B99990001.pdb be the same whether I > use automodel or loopmodel? > (provided I'm using the same optimizations and all, I'm just changing > the class name in the python script)
Yes. loopmodel is a subclass of automodel; by default it does the same thing as automodel, and then does additional loop refinement.
Ben Webb, Modeller Caretaker
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Mauricio Carrillo Tripp -
Modeller Caretaker