Dear Dr. Terwilliger,

Thanks for your reply. I divided my sequence into two and generated fragment files. These fragment file from Robetta have position numbers (highlighted in yellow) that I think are equivalent to the sequence number. For the second fragment file, should these numbers be changed to reflect the correct sequence number ? Or can the two fragments files be combined without correcting the position numbers ?

Thanks again

position: 1 neighbors: 200

1uyr A 25 T L -80.516 147.500 177.258 -0.178 4.758 48.053 3 0.000 P 1 F 1

1uyr A 26 Y L -64.648 133.444 -172.949 -0.178 4.758 48.053 3 0.000 P 1 F 1

1uyr A 27 V H -51.521 -44.146 -175.896 -0.178 4.758 48.053 3 0.000 P 1 F 1

1jr7 A 150 T L -84.574 -18.428 -173.610 -0.326 4.504 48.213 4 0.000 P 1 F 2

1jr7 A 151 Y L -104.837 12.859 175.722 -0.326 4.504 48.213 4 0.000 P 1 F 2

1jr7 A 152 V L -128.310 164.018 -178.953 -0.326 4.504 48.213 4 0.000 P 1 F 2

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Message: 4
Date: Tue, 7 Jun 2011 15:19:06 -0600 (MDT)
From: "Thomas C. Terwilliger" <terwilliger@lanl.gov>
To: "PHENIX user mailing list" <phenixbb@phenix-online.org>
Subject: Re: [phenixbb] Fragment library for mr_rosetta
Message-ID: <60860.128.165.0.81.1307481546.squirrel@webmail.lanl.gov>
Content-Type: text/plain;charset=iso-8859-1

Hi Doreen,

Yes, that should work fine...just paste the resulting files together after
deleting the header on all but the first (the files are just a list of
fragments)

All the best,
Tom T

>> Hi Everyone,
>>
>>
>> I am trying to generate a fragment library for my sequence of interest to
>> use with mr_rosetta. The Robetta server has a sequence limit of 650 amino
>> acids. For longer sequence, will it make sense to divide the sequence into
>> 650 amino acid fragments and generate multiple fragment files ?
>> Thanks
>>
>>
>> Thanks
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb@phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>

On Tue, Jun 7, 2011 at 4:48 PM, riya doreen <driya28@gmail.com> wrote:

Hi Everyone,

I am trying to generate a fragment library for my sequence of interest to use with mr_rosetta. The Robetta server has a sequence limit of 650 amino acids. For longer sequence, will it make sense to divide the sequence into 650 amino acid fragments and generate multiple fragment files ?

Thanks

Thanks