[phenixbb] sculptor
Dr G. Bunkoczi
gb360 at cam.ac.uk
Fri Nov 19 02:16:37 PST 2010
>"Sorry: Wrong alignment format:"
I agree that the message is not very helpful. I will change the parser so
that you get something more informative!
>CLUSTAL format alignment by MAFFT L-INS-i (v6.833b)
>
>
> gi|16132042|ref
> --ANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTI
> gi|157163695|re
> --ANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTI
In this case, the problem is that the CLUSTAL header is not what the parser
expects - I was not aware that there are so many .aln-like formats out
there. Fortunately, this is just a simple fix.
> Yes, and the target sequence (i.e. the protein that you crystallized)
> needs to be first. One annoying thing about MUSCLE is that it sorts
> sequences and (currently) won't let you disable this behavior, so you may
> need to do some cut-and-pasting. Maybe we need to modify the Python
> wrapper to do this automatically. (Although I think it would be even
> easier if Sculptor did the alignment automatically.)
There is already some alignment functionality in Sculptor, but it is not
very sophisticated (this is why you could use an external alignment is you
want full controll). Just specify a target sequence and the chain id in the
PDB-file you want to align the sequence with, and it does the rest.
It seems to be a common property of alignment programs to rearrange the
sequences, and I am wondering what would be more convenient from the user
perspective. We could in principle write wrappers for programs that come
with PHENIX so that the order of sequences stays the same, but this will
not solve the problem for external alignments. Would it be sufficient to
provide an option, so that one can specify the index of the target sequence
in the alignment file? Would it be better to provide the target sequence,
and let Sculptor figure out the index itself?
BW, Gabor
--
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Dr Gabor Bunkoczi
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building
Addenbrooke's Hospital
Hills Road
Cambridge CB2 0XY
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