Can I calculate the "Objective Function" based on a PDB without doing the comparative modelling?
The "Objective Function" is automatically shown on the second line of remark after doing the MODELLER comparative modelling.
Now I have a structure generated by RosettaCM, and I want to use the MODELLER's "Objective Function" to evaluate its reliability. Would it be possible?
Thank you!
On 6/13/20 7:08 PM, ZHANG Cheng via modeller_usage wrote: > Now I have a structure generated by RosettaCM, and I want to use the > MODELLER's "Objective Function" to evaluate its reliability. Would it be > possible?
The objective function scores how well the model fits the set of Modeller restraints. It wouldn't tell you anything useful for a model built using another technique. It sounds like what you're looking for is a model evaluation method, such as DOPE: https://salilab.org/modeller/9.24/manual/node259.html or SOAP: https://salilab.org/modeller/9.24/manual/node283.html
There's also a web server at https://salilab.org/evaluation/
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
ZHANG Cheng