Hello: 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.
I found that sometimes the PDF score can be negative such as: -20. Will this a good model?
THX
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
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@salilab.org 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@salilab.org http://www.salilab.org/modeller/ >Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >_______________________________________________ >modeller_usage mailing list >modeller_usage@salilab.org >https://salilab.org/mailman/listinfo/modeller_usage
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albert -
Modeller Caretaker