[Chimera-users] Question re editing alignments

Eric Pettersen pett at cgl.ucsf.edu
Thu Oct 27 10:55:33 PDT 2005

Hi Grant,
     The editing facilities in Multalign Viewer are somewhat basic  
and could stand improvement (e.g. undo would be nice).  You can only  
move a region in a certain direction if there is a gap somewhere  
ahead of the region that can be removed and placed behind the moving  
region.  MAV won't increase the length of your alignment (by placing  
an all-gap column on the end) in order to allow the motion [this is  
mentioned in the docs].
     A workaround is to save your alignment to a file and edit the  
file to add the all-gap columns necessary to allow your motion.  I  
would suggest FASTA or PIR formats, since those are the simplest to  
change.  Of course, at that point you may be able to make all the  
changes you want with a text editor and just cut MAV out of the loop  
-- it would depend on what you're doing.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On Oct 27, 2005, at 4:09 AM, Grant Jacobs wrote:

> While the help notes for the alignment editor says that gaps can be
> created, I can't see how! Surely I'm missing something...
> Selecting a residue or set of residues to create a region, then
> applying ctrl-left-arrow (or right arrow) yields an error complaining
> of a lack of gaps in the region ("No gap available in <seq name>").
> This makes me think that regions can only be moved if they are
> already bounded by gaps. Which in turn leaves me stumped as how to
> create the initial gaps manually...!
> What I had expected was for it to insert new gaps to the let of the
> region if applying ctrl-right-arrow to a region and vice versa for
> using ctrl-left-arrow.
> I'm using 2.180 on Mac OS X 10.4.2
> Grant
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