Re: [modeller_usage] PDF score question

[albert <leuven AT yeah.net>]

thank you very much for reply.
but in the loop model protocol, it always use PDF for scoring. How can I use DOPE score for loop model assessment?

THX
At 2012-03-03 02:23:03,"Modeller Caretaker" <modeller-care@ucsf.edu> wrote:
>On 3/2/12 9:59 AM, albert wrote:
>> As far as we know the lower DOPE score, the better model. I am wondering
>> how about the PDF score? also the lower score, the better model? eg:
>> model A PDF=200 is better than model B PDF score=300.
>
>The molecular PDF is simply the sum of restraint violations. So the 
>lower the PDF, the less the restraints are violated. This typically 
>means a good model, assuming that the restraints are an accurate 
>description of reality (assessment scores such as DOPE are typically 
>more reliable).
>
>    Ben Webb, Modeller Caretaker
>-- 
>modeller-care@ucsf.edu             http://www.salilab.org/modeller/
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