[Chimera-users] Chain/Structure ID as label
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
> can also work for the time being.
> >/ tile
> />/ labelopt info molecule
> />/ la @/serialNumber=1/
> 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.
> 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.
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