Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 25

[Ashish Runthala <ashishr AT bits-pilani.ac.in>]

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 AT salilab.org>
To: "modeller usage" <modeller_usage@listsrv.ucsf.edu>
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 AT yeah.net>
To: "Min-yi Shen" <minyishen AT gmail.com>,	modeller_usage
	<modeller_usage@listsrv.ucsf.edu>
Subject: Re: [modeller_usage] PDF score question
Message-ID: <1395e154.a0b.135d7345e05.Coremail.leuven AT 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 AT gmail.com> wrote:
>Just calculate the DOPE score for all loop models.
>
>On Fri, Mar 2, 2012 at 9:15 PM, albert <leuven AT 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@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/
>>>Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
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Message: 2
Date: Sat, 03 Mar 2012 08:31:42 -0800
From: Modeller Caretaker <modeller-care@ucsf.edu>
To: albert <leuven AT yeah.net>
Cc: modeller_usage <modeller_usage@listsrv.ucsf.edu>,	Min-yi Shen
	<minyishen AT gmail.com>
Subject: Re: [modeller_usage] PDF score question
Message-ID: <4F52476E.2030709 AT salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 3/2/12 10:17 PM, albert wrote:
> 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.

Just set loop_assess_methods=assess.DOPE when you set up your loopmodel 
object, similar to assess_methods for automodel:
http://salilab.org/modeller/9.10/manual/node77.html

	Ben Webb, Modeller Caretaker
-- 
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage


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