[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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