JCSG@SSRL, SLAC
Phone: (650) 926-2992
Fax: (650) 926-3292
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 followVDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDDtitle text for sequence of template (supplied PDB) to follow-AFSGTWQVYAQENYEEFLRAISLPEEVIKLAKDVKPVTEIQQNGSDFTITSKTPGKTVTNSFTIGKEAEIT--TMDG All the best, Tom TSomebody 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_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb