On Thu, Nov 18, 2010 at 2:31 PM, Bryan Lepore <bryanlepore@gmail.com> wrote:
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