Re: [phenixbb] Fragment library for mr_rosetta

Hi Riya, As you suspected, you should change the sequence position numbers to reflect the correct sequence number. All the best, Tom

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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

--------- Message: 4 Date: Tue, 7 Jun 2011 15:19:06 -0600 (MDT) From: "Thomas C. Terwilliger" To: "PHENIX user mailing list" Subject: Re: [phenixbb] Fragment library for mr_rosetta Message-ID: <[email protected]> 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

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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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

On Tue, Jun 7, 2011 at 4:48 PM, riya doreen wrote:

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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