On Thu, Nov 18, 2010 at 2:31 PM, Bryan Lepore
I am checking out sculptor, looks pretty cool, but I provided what i thought was a clustal format alignment to sculptor using --verbose, and it reports
"Sorry: Wrong alignment format:"
that's it. sounds like user error, but i'm not sure where to proceed next. i tried mafft and clustalw2 output for this. a sample of a bit of the top of the .aln is below.
CLUSTAL format alignment by MAFFT L-INS-i (v6.833b)
gi|16132042|ref --ANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTI gi|157163695|re --ANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTI
I just looked at the parser code, and I think it is expecting exactly the same output as CLUSTALW, which has a slightly different first line than MAFFT. We now distribute a multiple sequence alignment program called MUSCLE with Phenix - you can use it like this: phenix.muscle -in seqs.fa -out seqs.aln -clwstrict I hope this fixes it - if not, Sculptor should also take alignments in FASTA or PIR format. (Make sure you use the correct file extension, because this is what it uses to decide how to parse a file.) -Nat