[Chimera-users] Chain/Structure ID as label

Tom Goddard goddard at sonic.net
Thu Feb 24 12:30:41 PST 2011

Hi Berhane,

   I don't know of a way to do this currently in Chimera.  I have heard 
the same request to have labels for tiled 2-d electron microscopy maps 
from Javier Velazquez-Muriel.

   It would be possible to improve the "tile" command so it could place 
the labels as 2D labels.  But the problem is that those labels would no 
longer align with the model if you zoom the view or translate the view 
in x or y, because 2d labels are fixed in their 2d window position.  
After tiling, it is often helpful to resize the window and possibly 
zoom.  Possibly the tile command could try to keep moving the 2D labels 
so the keep the correct position.  An alternative is to use 3d labels 
that are attached to atoms.  The problem there is that there is no atom 
to attach the label to for density maps, also the label should not bob 
around to different positions if you rotate, which would require 
attaching it to an atom at the center of rotation.  Some marker atoms 
could handle that I guess.  But I think the atom would have to be shown 
for the label to appear.  So there are some technical difficulties.  
Basically the underlying support for the type of labels you want isn't 
in Chimera.


> Hi,
> I often read in 1-30 hydrogen-bonded molecular clusters from XYZ files 
> and tile them for analysis. It would be great to label 
> each cluster/model with its chain ID or file name.  Labeling them 
> using the 2Dlabel command is inconvenient especially when I have a 
> large number of models.
> Is there an easy way of doing this?
> Thanks in advance.
> Berhane

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