[phenixbb] mr_rosetta

[Abhinav Kumar]

Thanks Tom.
I guess the file terminator line '--' was missing.
It seems to be working fine now.

A quick question: If I use the other simpler format, does its file 
extension need to be different or will .ali do?

Thanks,
Abhinav

JCSG at SSRL, SLAC
Phone: (650) 926-2992
Fax: (650) 926-3292


On 10/11/2011 12:57 PM, Thomas C. Terwilliger wrote:
> 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
>>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20111011/f9674e3e/attachment.htm>