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A few additions to that 3d label solution can improve it a bit:<br>
<span class="Apple-style-span" style="font-family: Verdana;
font-size: medium;">
<pre style="white-space: pre-wrap; word-wrap: break-word;"><i>tile
</i><i>labelopt info molecule
</i><i>la offset 0,-20,0 @/serialNumber=1
color white,la @/serialNumber=1</i></pre>
</span><br>
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), ....<br>
<br>
Tom<br>
<br>
<blockquote type="cite">Thanks a lot, Tom.
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<div>Coupling 'tile' and '2dlabels'` in an automated way sounds
like a good solution. I will try to figure out a way to do
that.</div>
<div><br>
</div>
<div>A solution suggested earlier (<a
href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-July/004083.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-July/004083.html</a>)
can also work for the time being.</div>
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<span class="Apple-style-span" style="font-family: Verdana;
font-size: medium;">
<pre style="white-space: pre-wrap; word-wrap: break-word;">><i> tile
</i>><i> labelopt info molecule
</i>><i> la @/serialNumber=1</i></pre>
</span>Best,</div>
<div>Berhane</div>
<div><br>
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<div>
<div class="gmail_quote">On Thu, Feb 24, 2011 at 3:30 PM, Tom
Goddard <span dir="ltr"></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hi Berhane,<br>
<br>
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.<br>
<br>
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.<br>
<font color="#888888">
<br>
Tom</font>
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<div><br>
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204,
204); padding-left: 1ex;">
Hi,<br>
<br>
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.<br>
<br>
Is there an easy way of doing this?<br>
<br>
Thanks in advance.<br>
Berhane<br>
<br>
</blockquote>
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