[Chimera-users] Can I use "Chimera" to measure length of a VRML file?

[Thomas Goddard]

Hi Masako,

  Chimera reads VRML files but does not support all of the VRML
format.  If Chimera correctly displays your VRML model you can measure
a length.  You can't directly measure the VRML.  You would have to
trace a new path using the VRML as a guide and measure that path in
Chimera.  You would use the Volume Path Tracer tool which allows you
to place a chain of markers.  The path tracer dialog is shown with
menu entry

	Tools / Volume Data / Volume Path Tracer

You'll need to turn on the "Drop markers on empty space" option and
the "Move markers with mouse" option.  Then you can place a marker with
the mouse and drag it to the location you want.  The path tracer tool
only knows how to automatically position markers in the z-direction
(perpendicular to the screen) for volume data, not for VRML models.
So you will have to do that positioning by hand with the mouse.  Holding
down the Shift key while dragging the marker will move it in the z
direction.

  When you have placed markers on the VRML model to define the path you
would like to measure you can select the path (ie the links connecting
the markers) and use the keyboard shortcut "pl" to measure the lengths.
You'll need to turn on keyboard shortcuts using menu entry

	Tools / General Controls / Accelerators On

To select the path you want to measure use ctrl-left-mouse-button to
drag a box around the selected markers.  The markers and links will
be outlined in green.  Another approach is to ctrl-click on one of
the markers and use the "sc" keyboard shortcut to extend the selection
to all the connected links and markers.  The sc shortcut is in Chimera
version 1.2255 in the snapshots section of the Chimera download page
but not in 1.2199 production release version.

  I talked to Maryann Martone at the BioImage meeting about measuring
neural spine lengths.  If that is what you are looking at here are a
few additional ideas.  If you have 3-D microscopy data it would be
easier to place markers and trace paths directly on that data in
Chimera.  Chimera reads about a dozen volume map formats -- probably
MRC is the most commonly used.  If you use a format Chimera cannot
read I can look into adding it.

  Another idea is that if you have already traced the spines in other
software (maybe that is where the VRML came from?) then a text list of
xyz marker positions could be read into Chimera, avoiding the need to
retrace the structure in Chimera.  The format for importing the
markers into Chimera is described in the Chimera manual

	http://www.cgl.ucsf.edu/chimera/1.2199/docs/ContributedSoftware/volumepathtracer/framevolpath.html

and is a text file using XML syntax.

  Let me know if you have further questions.

	Tom