thanks for reply. But I don't think there is a independent script in Modeller to do so. It should be add something in the loop model generating steps.
At 2012-03-03 14:14:23,"Min-yi Shen" <> wrote:
>Just calculate the DOPE score for all loop models.
>
>On Fri, Mar 2, 2012 at 9:15 PM, albert <> wrote:
>> 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" <>
>> 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
>>>--
>>> ! http://www.salilab.org/modeller/
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>>
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