Dear Albert, As Sir Ben has told, you may use loop_assess_methods=(assess.DOPE, assess.GA341,assess.normalized_dope) You will get the entire set of assessment data for your compiled set of models. Keep the number higher to best span the features of the utmost possibly traced conformational span of the loop atoms.

Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

----- Original Message ----- From: "modeller usage-request" modeller_usage-request@salilab.org To: "modeller usage" modeller_usage@salilab.org Sent: Saturday, March 3, 2012 10:01:59 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 11, Issue 25

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Today's Topics:

1. Re: PDF score question (albert) 2. Re: PDF score question (Modeller Caretaker)

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Message: 1 Date: Sat, 3 Mar 2012 14:17:07 +0800 (CST) From: albert leuven@yeah.net To: "Min-yi Shen" minyishen@gmail.com, modeller_usage modeller_usage@salilab.org Subject: Re: [modeller_usage] PDF score question Message-ID: 1395e154.a0b.135d7345e05.Coremail.leuven@yeah.net Content-Type: text/plain; charset="gbk"

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" minyishen@gmail.com wrote: >Just calculate the DOPE score for all loop models. > >On Fri, Mar 2, 2012 at 9:15 PM, albert leuven@yeah.net 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" 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 >> >> >> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage@salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage >>