can i compare th DOPE score of my mode with dope score of X-ray PDB.?if i can, what should be the DOPE SCORE difference between my model and X-ray PDB in order tobe my model is a reliable model. could you please tell some difference in score value yhanks in advance

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Today's Topics:

1. Re: superpose.py (vidhya sankar)

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Message: 1 Date: Thu, 16 Aug 2007 01:00:44 -0700 (PDT) From: vidhya sankar Subject: Re: [modeller_usage] superpose.py To: modeller_usage@salilab.org Message-ID: 467087.77948.qm@web51604.mail.re2.yahoo.com Content-Type: text/plain; charset="iso-8859-1"

i do not have proper PDB TEMPLATE for my 529 amino acid sequence.I have only the PDB of 53% sequence similiarity & identity. upon using this in superpose .py script i have got RMS OF 2.3337 and number of aligned equivalent positions 33 amog 115 residues will it be reliable value ?

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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@salilab.org Message-ID: 267539.63819.qm@web51610.mail.re2.yahoo.com 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

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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