[phenixbb] mr_rosetta

[Thomas C. Terwilliger]

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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