[Chimera-users] Chimera 3D labels

[Elaine Meng]

On Feb 16, 2009, at 6:53 AM, nettles wrote:
>
> Dear Elaine,
> I'm thinking this should be possible, but don't know how to do it.   
> Can the labeling function in Chimera could be made more spacially  
> flexible?
>
> An example is below. The residue label coordinates are anchored to  
> a fixed 3D point that may, or may not be desirable for a given  
> view. Can this be adjusted?
>
> It looks like these references may be set at centroids. Maybe one  
> could have a toggle switch that sets the anchor projected a certain  
> distance from a C-alpha along the viewing vector. That might  give  
> quick access unified text float-over
>
> Thanks again for such a great tool.
> Jim

[attachment removed by Elaine]

Dear Jim,
I am frequently irked by the same issue.  Currently residue labels  
are anchored at the centroid of the displayed atoms, whereas  
sometimes it would look better if they were anchored at the alpha- 
carbon.  I've previously created a bug report about this.  Longer  
term we would also like them to be movable with the mouse, but that  
also can't be done currently.

Here is the bug/request tracking info:
http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/6866
http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/167

One current workaround is that you can label some particular atom in  
the residue with residue information.  However, currently that atom  
must be explicitly displayed (won't work to label some backbone atom  
if ribbon is shown and suppresses that atom... which I've also  
complained about!). Commands to do that:

labelopt info residue
la @ca

[or if ribbon is shown, "la @cb" instead if you can live without the  
glycine residue labels]

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                       http://www.cgl.ucsf.edu/home/meng/index.html