[Chimera-users] Chain/Structure ID as label

Tom Goddard goddard at sonic.net
Fri Feb 25 09:38:05 PST 2011

A few additions to that 3d label solution can improve it a bit:

//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), ....


> 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

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