A few additions to that 3d label solution can improve it a bit:
tile
labelopt info molecule
la offset 0,-20,0 @/serialNumber=1
color white,la @/serialNumber=1

Here I added the offset which will place the label 20 Angstroms below atom number 1 on the screen.  That hopefully puts it below the molecule where it won't be obscured.  And I added the color command to make the label white (assuming you use black background).  Otherwise the label color matches the atom color which maybe blue (nitrogen), red (oxygen), ....

    Tom

Thanks a lot, Tom.

Coupling 'tile' and '2dlabels'` in an automated way sounds like a good solution. I will try to figure out a way to do that.

A solution suggested earlier (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-July/004083.html) can also work for the time being.
> tile
> labelopt info molecule
> la @/serialNumber=1
Best,
Berhane

On Thu, Feb 24, 2011 at 3:30 PM, Tom Goddard  wrote:
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.

   Tom



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