Re: [modeller_usage] dope calculations

To:

Subject: Re: [modeller_usage] dope calculations

From: vidhya sankar <>

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

wrote:

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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:
Message-ID: <>
Content-Type: text/plain; charset="iso-8859-1"

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

wrote:
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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:
Message-ID: <>
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
--
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:
Message-ID: <>
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:
Message-ID: <>
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:
Message-ID: <>
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:
Message-ID: <>
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
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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