[Chimera-users] labels in Chimera

[Thomas Goddard]

Hi Sergey,

  You can use the Volume Path Tracer tool to put labels near parts of one
or more density maps.  Path Tracer is designed for putting markers on
high density regions but it allows you to place them anywhere (in 3D),
and you can put any label text next to a marker.  The path tracer dialog
is shown with menu entry

	Tools / Volume Data / Volume Path Tracer

Start by changing some settings.  Turn off "Place markers on spots
with mouse".  That is for placing marker on high density regions.
Turn on "Drop markers on empty space with mouse".  That allows you to
place a marker anywhere, for example next to a density blob.  Turn on
"Move markers with mouse".  This will allow you to reposition the
markers and their attached label.  Use button 3 with the ctrl keyboard
key held down to place a marker.  Click on the "Markers" button at the
top of the path tracer dialog to see some more options in the dialog.
Type in a "Marker note" and press Return to see it displayed next to
the marker.  The radius of the marker sphere can be made so small it
is invisible (0.0001) but the value has to be > 0.  The text can be
given whatever color you want using the color button at the end of the
dialog line containing "Marker Note".  When changing marker note or
radius you need to select it first in the graphics window (click on it
or drag over it with ctrl button 1) so that it is shown with a green
outline.  To move the marker hold down ctrl while pressing button 3
on top of it and drag it.  Holding down the ctrl and shift key lets
you move it in and out of the screen.  There is no control of label
size or font currently although if you were saving an image you could
make the Chimera window small so that the text is relatively large and
use File / Save Image to save at whatever image resolution you want.

  Besides using labels you can of course give different density maps
different colors to distinguish them.  Use the color button in the
volume viewer dialog for that.  You can also color different blobs
in the same density map with different colors.  To do that you would
place markers on the blobs as described above, give colors to those
markers, and then use the Color Zone tool (menu entry Tools / Volume Data /
Color Zone) to color parts of the surface within a give range of the
markers to match the marker color.  Lastly, if your blobs are not connected
to one another you can do the coloring just by clicking on them using
the prerelease "color surface pieces" features
(http://www.cgl.ucsf.edu/chimera/prerelease/prerelease.html).

	Tom