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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@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@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
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