[phenixbb] sculptor

[Dr G. Bunkoczi]

>"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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