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Re: [modeller_usage] dope calculations
- To: modeller_usage@listsrv.ucsf.edu
- Subject: Re: [modeller_usage] dope calculations
- From: vidhya sankar <scvsankar_agr AT yahoo.com>
- Date: Mon, 13 Aug 2007 06:43:54 -0700 (PDT)
dear sir ,
i do not have proper PDB TEMPLATE for my 529 amino acid sequence.I have only the PDB of 53% sequence similiarity & identity. can i take this Template to compare My DOPE score with PDB.WILL IT BE RELIABLE value? i am expecting your reply
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Today's Topics:
1. Re: log files (vidhya sankar)
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Message: 1
Date: Sat, 11 Aug 2007 04:21:41 -0700 (PDT)
From: vidhya sankar
Subject: Re: [modeller_usage] log files
To: modeller_usage@listsrv.ucsf.edu
Message-ID: <267539.63819.qm AT web51610.mail.re2.yahoo.com>
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i did not get any log files when i run modeller9v1 in windowsXp .what shoul i do to get log files thank you? i am expecting your reply
modeller_usage-request AT salilab.org wrote:
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When replying, please edit your Subject line so it is more specific
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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@listsrv.ucsf.edu
Message-ID: <46BB71B6.8070207 AT 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@ucsf.edu http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 2
Date: Fri, 10 Aug 2007 05:10:48 -0700 (PDT)
From: vidhya sankar
Subject: [modeller_usage] regarding DOPE score
To: modeller_usage@listsrv.ucsf.edu
Message-ID: <835492.28231.qm AT 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@listsrv.ucsf.edu
Message-ID: <748909.620.qm AT 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@listsrv.ucsf.edu
Message-ID: <999038.6025.qm AT 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@listsrv.ucsf.edu
Message-ID: <46BCB3A5.6020703 AT 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@ucsf.edu http://www.salilab.org/modeller/
Modeller mail list:
http://salilab.org/mailman/listinfo/modeller_usage
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