[phenixbb] Fragment library for mr_rosetta

Thomas C. Terwilliger terwilliger at lanl.gov
Thu Jun 9 17:19:10 PDT 2011


Hi Riya,

As you suspected, you should  change the sequence position numbers to
reflect the
 correct sequence number.

All the best,
Tom


>> 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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