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Today's Topics:

1. Re: DOPE (Modeller Caretaker)
2. regarding DOPE score (vidhya sankar)
3. regrding superpose.py (vidhya sankar)
4. ref: SUPERPOSE.PY (vidhya sankar)
5. Re: regarding DOPE score (Modeller Caretaker)


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Message: 1
Date: Thu, 09 Aug 2007 12:57:42 -0700
From: Modeller Caretaker
Subject: Re: [modeller_usage] DOPE
To: Ester Fust? Dom?nguez
Cc: modeller_usage@salilab.org
Message-ID: <46BB71B6.8070207@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Ester Fust? Dom?nguez wrote:
> How can I see the DOPE score profile? I don't know how to use
> *assess_dope* command.

There is an example at the end of the basic tutorial at
http://salilab.org/modeller/tutorial/basic.html

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


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Message: 2
Date: Fri, 10 Aug 2007 05:10:48 -0700 (PDT)
From: vidhya sankar
Subject: [modeller_usage] regarding DOPE score
To: modeller_usage@salilab.org
Message-ID: <835492.28231.qm@web51612.mail.re2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

i have got a DOPE score of -41275.816406 is it reliable value ? .how can i come to conclusions for my 3Dmodel .how can i analyse DOPE SCORE

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Message: 3
Date: Fri, 10 Aug 2007 06:12:02 -0700 (PDT)
From: vidhya sankar
Subject: [modeller_usage] regrding superpose.py
To: modeller_usage@salilab.org
Message-ID: <748909.620.qm@web51605.mail.re2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

I have got a RMS and DRMS value of after super position 2.0482 and 1.5631 respectively.is it reliable value? .for 53.85% sequence identity i am expecting your reply

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Message: 4
Date: Fri, 10 Aug 2007 06:13:48 -0700 (PDT)
From: vidhya sankar
Subject: [modeller_usage] ref: SUPERPOSE.PY
To: modeller_usage@salilab.org
Message-ID: <999038.6025.qm@web51601.mail.re2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

I have got a RMS and DRMS value of after super position 2.0482 and 1.5631 respectively.is it reliable value? .for 53.85% sequence identity i am expecting your reply

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Message: 5
Date: Fri, 10 Aug 2007 11:51:17 -0700
From: Modeller Caretaker
Subject: Re: [modeller_usage] regarding DOPE score
To: vidhya sankar
Cc: modeller_usage@salilab.org
Message-ID: <46BCB3A5.6020703@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

vidhya sankar wrote:
> i have got a DOPE score of -41275.816406 is it reliable value ? .how
> can i come to conclusions for my 3Dmodel .how can i analyse DOPE SCORE

The absolute value is essentially meaningless, so you can use it only to
compare against other models of the same sequence, just like the
Modeller molpdf score. See
http://salilab.org/modeller/9v2/manual/node245.html

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


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End of modeller_usage Digest, Vol 6, Issue 75
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