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