[phenixbb] sculptor

Nathaniel Echols nechols at lbl.gov
Fri Nov 19 10:12:35 PST 2010

On Fri, Nov 19, 2010 at 4:22 AM, Jovine Luca <luca.jovine at ki.se> wrote:

> This is actually a bit odd, since one could run version 3.7 of MUSCLE with
> a -stable flag that would output sequences in the the same order as the
> input... but apparently this has been disabled in the version that ships
> with PHENIX (3.8.31). Maybe we could just ask Robert Edgar to put it back?

Yeah, I'll ask him about this.  Unfortunately we needed a bug fix in 3.8,
otherwise I might have left it alone.

But I still think the solution is to do the alignment internally - the user
should be able to provide a PDB file and a target sequence, and the program
will run MUSCLE automatically and figure out which row in the alignment
output corresponds to each sequence.  This avoids an extra step and would
clear up the confusion regarding formats, ordering, etc.

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