[phenixbb] mr_rosetta

[Thomas C. Terwilliger]

Hi Abhinav,
Sorry, I should have said exactly 6 lines (the -- counts).
-Tom
>> Hi Abhinav,
>>
>> This format is very unforgiving. It has to have exactly 5 lines:
>>
>> ## TARGET SP_3n91
>> # hhsearch
>> scores_from_program: 0 1.00
>> 0  --DDDEVTMNSK....
>> 0  GSDNEFPDFDYQ....
>> --
>>
>> also note I changed SP 3n91 to SP_3n91. Your PDB file name must also start
>> with SP_3n91 in this case.  You need a pdb file name with at least 5 chars
>> before the ".pdb" and these 5 characters have to match the 5 characters
>> after TARGET on the first line.
>>
>> Note that the other format read by mr_rosetta is a lot easier:
>>
>>> title text for sequence of target to follow
>> VDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDD
>>> title text for sequence of template (supplied PDB) to follow
>> -AFSGTWQVYAQENYEEFLRAISLPEEVIKLAKDVKPVTEIQQNGSDFTITSKTPGKTVTNSFTIGKEAEIT--TMDG
>>
>>
>> All the best,
>> Tom T
>>
>>>> Somebody helped me out with the format. Thanks.
>>>> My alignment file looks like:
>>>> ## SP 3n91
>>>>
>>>>
>>>> 0  --DDDEVTMNSK....
>>>> 0  GSDNEFPDFDYQ....
>>>>
>>>>
>>>>
>>>> But phenix says
>>>>
>>>> ******************* ERROR ENDING ***************
>>>>
>>>> Sorry, the alignment file ['xx.ali']
>>>> does not seem to have the correct format?
>>>> It can either start with '##' or with '> title of target seq here'
>>>>
>>>> ******************* ERROR ENDING ***************
>>>>
>>>> I do have the file starting with '##'!
>>>>
>>>> Thanks,
>>>> Abhinav
>>>>
>>>> JCSG at SSRL, SLAC
>>>> Phone: (650) 926-2992
>>>> Fax: (650) 926-3292
>>>>
>>>>
>>>> On 10/11/2011 12:23 PM, Abhinav Kumar wrote:
>>>>> Hi,
>>>>>
>>>>> I am looking for file format for alignment file (*.ali) used in
>>>>> mr_rosetta.
>>>>> The description on the Phenix web site is not clear.
>>>>> Can someone please describe  the file format with an example?
>>>>> --
>>>>>
>>>>> Thanks,
>>>>> Abhinav
>>>>>
>>>>> JCSG at SSRL, SLAC
>>>>> Phone: (650) 926-2992
>>>>> Fax: (650) 926-3292
>>>>>
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>>>>
>>
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