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/ ContributedSoftware/multalignviewer/defineheader.html#headerformat 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 Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu