[Chimera-users] MultiAlign viewer

Eric Pettersen pett at cgl.ucsf.edu
Tue Nov 14 16:28:47 PST 2006

On Nov 10, 2006, at 8:22 AM, Mireille Krier wrote:

> Dear all,
> I want to add to the header of a sequence alignment graphical
> representations such as cylinders and thick arrows to symbolize
> stretches of helix and strand.
> Is this possible? Should one annotate this in the Stockholm format
> file (and if yes could you provide me an example file) ?

	Sorry for the slow response, but Friday was a holiday here and  
Monday was very busy (the NIH was site-visiting us).  The shortest  
answer is no, Multalign Viewer can't yet depict graphics in its  
header lines (except for histograms).  Assuming you are trying to  
develop a figure for a paper, some alternatives are ALSCRIPT (http:// 
www.compbio.dundee.ac.uk/Software/Alscript/alscript.html) and ESPript  
(http://espript.ibcp.fr//ESPript/ESPript/).  Perhaps others on the  
list can suggest more.
	That said, one of my highest development priorities for Multalign  
Viewer is to make such graphical headers available (the other being  
dendrogram support).  Nonetheless, it will take months to implement  
and deploy that feature, so you should use something else until then.
	If you aren't doing this for a paper, you can already insert your  
own alphanumeric or histogram headers if that's good enough.  That's  
described here:  http://www.cgl.ucsf.edu/chimera/docs/ 
	Also, GC markups in Stockholm files are displayed as headers.
	I'm glad you spoke up since although I get a good amount of feedback  
from users here at UCSF, I don't get as much opportunity to hear the  
needs of other users.  Feel free to mention other things you'd like  
to see implemented.


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

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