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

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        pett@cgl.ucsf.edu

                        http://www.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
-- 
-------------------------------------------------------------------
Grant Jacobs Ph.D.                                     BioinfoTools
ph. +64 3 478 0095  (office, after 10am)               PO Box 6129,
or  +64 27 601 5917 (mobile)                               Dunedin,
gjacobs@bioinfotools.com                               NEW ZEALAND.
    Bioinformatics tools: deriving knowledge from biological data
Bioinformatics tools - software development - consulting - training
  15 years experience in bioinformatics ready to solve your problem
Check out the website for more details: http://www.bioinfotools.com

The information contained in this mail message is  confidential and
may be legally privileged.  Readers of this message who are not the
intended recipient are hereby notified that any use, dissemination,
distribution or reproduction of this message is prohibited.  If you
have received this message in error please notify the sender immed-
iately and destroy the original message.  This applies also to  any
attached documents.
_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users