[phenixbb] Fragment library for mr_rosetta

[riya doreen]

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" <terwilliger at lanl.gov>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Fragment library for mr_rosetta
Message-ID: <60860.128.165.0.81.1307481546.squirrel at 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 at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>

On Tue, Jun 7, 2011 at 4:48 PM, riya doreen <driya28 at 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
>
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